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/7769801/working' mkdir: created directory `/scratch/stefan/7769801/working/protonate' Storing results in /scratch/stefan/7769801/finished Working in /scratch/stefan/7769801/working /scratch/stefan/7769801/working /scratch/stefan/7769801 /scratch/stefan/7769801/working/protonate /scratch/stefan/7769801/working /scratch/stefan/7769801 Precomputing protomers for all compounds (pH: 7.4) awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) chmod: cannot operate on dangling symlink `/nfs/home/stefan/.install4j' rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory Nov 27, 2019 6:17:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:26 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:22:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. ph 7.4: 1037 protomers created Coalesing and merging protomers 1015 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1015 protomers after new stereo-center expansion /scratch/stefan/7769801/working /scratch/stefan/7769801 Bulk generating 3D conformations all protomers in /scratch/stefan/7769801/working/3D mkdir: created directory `/scratch/stefan/7769801/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7769801/working/protonate/xaaaaim-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' 1016 3D conformations generated for 1000 compounds Building REAL300000220001 mkdir: created directory `/scratch/stefan/7769801/working/building' mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220001' /scratch/stefan/7769801/working/building/REAL300000220001 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220001 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220001/0 /scratch/stefan/7769801/working/building/REAL300000220001 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/1 `/scratch/stefan/7769801/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1) `REAL300000220001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220001 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 12, 44, 67, 67, 44, 73, 73, 44, 73, 73, 1, 7, 7, 7, 7, 7, 1, 1, 1, 44, 73, 73, 44, 73, 73, 1] 201 rigid atoms, others: [35, 36, 37, 44, 12, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 381 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220001 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73, 73, 73, 73, 14, 4, 1, 4, 6, 6, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 73, 73, 73, 4, 1, 1, 1, 1, 1, 73] 201 rigid atoms, others: [39, 40, 41, 42, 43, 19, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44]) total number of confs: 471 number of broken/clashed sets: 26 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220001 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 59, 164, 201, 201, 164, 201, 201, 164, 201, 201, 7, 1, 1, 1, 1, 1, 7, 7, 7, 164, 201, 201, 164, 201, 201, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 34, 32, 33, 30, 31] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 852 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220001 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220001 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 mkdir: created directory `/scratch/stefan/7769801/finished' Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220001/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220001 Building REAL300000220002 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220002' /scratch/stefan/7769801/working/building/REAL300000220002 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220002 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220002/0 /scratch/stefan/7769801/working/building/REAL300000220002 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/2 `/scratch/stefan/7769801/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C(F)=C3)C(=O)NC2=C1) `REAL300000220002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220002 none N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C(F)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220002 none N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C(F)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220002 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220002 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220002/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220002 Building REAL300000220003 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220003' /scratch/stefan/7769801/working/building/REAL300000220003 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220003 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220003/0 /scratch/stefan/7769801/working/building/REAL300000220003 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/3 `/scratch/stefan/7769801/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C=CC(=O)[O-])O3)C(=O)NC2=C1) `REAL300000220003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220003 none N#CC1=CC=C2C(=CC3=CC=C(C=CC(=O)[O-])O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 9, 9, 11, 11, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 9, 9, 8, 8] 17 rigid atoms, others: [7, 8, 9, 10, 11, 12, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) 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: REAL300000220003 none N#CC1=CC=C2C(=CC3=CC=C(C=CC(=O)[O-])O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 17, 17, 17, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 17, 17, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220003 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220003 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220003/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220003 Building REAL300000220004 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220004' /scratch/stefan/7769801/working/building/REAL300000220004 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220004 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220004/0 /scratch/stefan/7769801/working/building/REAL300000220004 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/4 `/scratch/stefan/7769801/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=C2C(=O)NC3=CC(C#N)=CC=C23)C=C1C(=O)[O-]) `REAL300000220004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220004 none COC1=CC=C(C=C2C(=O)NC3=CC(C#N)=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 7] 13 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 34, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220004 none COC1=CC=C(C=C2C(=O)NC3=CC(C#N)=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 7, 7, 7, 7, 7, 1] 13 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 19, 20, 21, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220004 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220004 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220004/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220004 Building REAL300000220005 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220005' /scratch/stefan/7769801/working/building/REAL300000220005 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220005 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220005/0 /scratch/stefan/7769801/working/building/REAL300000220005 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/5 `/scratch/stefan/7769801/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=CC=C3F)C(=O)NC2=C1) `REAL300000220005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220005 none N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=CC=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4] 4 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 9 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220005 none N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=CC=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28]) total number of confs: 5 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220005 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220005 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220005/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220005 Building REAL300000220006 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220006' /scratch/stefan/7769801/working/building/REAL300000220006 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220006 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220006/0 /scratch/stefan/7769801/working/building/REAL300000220006 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/6 `/scratch/stefan/7769801/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C(=O)[O-])C=C1C=C1C(=O)NC2=CC(C#N)=CC=C12) `REAL300000220006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220006 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 7, 7, 13, 7, 7, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 7, 13, 13, 13, 7, 1, 1, 1, 1, 1] 20 rigid atoms, others: [34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220006 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 1, 3, 3, 3, 1, 7, 7, 7, 7, 7] 20 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 11, 12, 13, 33, 29] set([0, 6, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220006 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220006 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220006/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220006 Building REAL300000220007 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220007' /scratch/stefan/7769801/working/building/REAL300000220007 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220007 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220007/0 /scratch/stefan/7769801/working/building/REAL300000220007 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/7 `/scratch/stefan/7769801/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(F)C(C(=O)[O-])=C3)C(=O)NC2=C1) `REAL300000220007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220007 none N#CC1=CC=C2C(=CC3=CC=C(F)C(C(=O)[O-])=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7] 7 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) 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: REAL300000220007 none N#CC1=CC=C2C(=CC3=CC=C(F)C(C(=O)[O-])=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28]) total number of confs: 8 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220007 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220007 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220007/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220007 Building REAL300000220008 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220008' /scratch/stefan/7769801/working/building/REAL300000220008 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220008 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220008/0 /scratch/stefan/7769801/working/building/REAL300000220008 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/8 `/scratch/stefan/7769801/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=C(CC(=O)[O-])C=C1) `REAL300000220008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220008 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 2, 2, 2, 2, 2, 1, 1, 2, 2, 1, 1] 3 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220008 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 2, 2, 3, 3, 2, 2] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27] set([32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 9 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220008 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220008 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220008/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220008 Building REAL300000220009 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220009' /scratch/stefan/7769801/working/building/REAL300000220009 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220009 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220009/0 /scratch/stefan/7769801/working/building/REAL300000220009 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/9 `/scratch/stefan/7769801/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC(Br)=CC(C(=O)[O-])=C3)C(=O)NC2=C1) `REAL300000220009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220009 none N#CC1=CC=C2C(=CC3=CC(Br)=CC(C(=O)[O-])=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4] 4 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220009 none N#CC1=CC=C2C(=CC3=CC(Br)=CC(C(=O)[O-])=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28]) total number of confs: 5 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220009 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220009 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220009/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220009 Building REAL300000220010 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220010' /scratch/stefan/7769801/working/building/REAL300000220010 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220010 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220010/0 /scratch/stefan/7769801/working/building/REAL300000220010 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/10 `/scratch/stefan/7769801/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C=CC(=O)[O-])C=C3)C(=O)NC2=C1) `REAL300000220010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220010 none N#CC1=CC=C2C(=CC3=CC=C(C=CC(=O)[O-])C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 4, 4, 1, 1, 4, 4] 5 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 17, 18, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34]) total number of confs: 17 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: REAL300000220010 none N#CC1=CC=C2C(=CC3=CC=C(C=CC(=O)[O-])C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 2, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 4, 4, 1, 1] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31]) total number of confs: 17 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220010 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220010 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220010/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220010 Building REAL300000220011 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220011' /scratch/stefan/7769801/working/building/REAL300000220011 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220011 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220011/0 /scratch/stefan/7769801/working/building/REAL300000220011 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/11 `/scratch/stefan/7769801/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC(F)=C(C(=O)[O-])C=C3F)C(=O)NC2=C1) `REAL300000220011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220011 none N#CC1=CC=C2C(=CC3=CC(F)=C(C(=O)[O-])C=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220011 none N#CC1=CC=C2C(=CC3=CC(F)=C(C(=O)[O-])C=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220011 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220011 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220011/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220011 Building REAL300000220012 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220012' /scratch/stefan/7769801/working/building/REAL300000220012 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220012 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220012/0 /scratch/stefan/7769801/working/building/REAL300000220012 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/12 `/scratch/stefan/7769801/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=C2C(=CC=C1)NN=C2C(=O)[O-]) `REAL300000220012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220012 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=C2C(=CC=C1)NN=C2C(=O)[O-] NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 1, 1, 1, 1] 5 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220012 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=C2C(=CC=C1)NN=C2C(=O)[O-] NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29] set([32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 6 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220012 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220012 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220012/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220012 Building REAL300000220013 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220013' /scratch/stefan/7769801/working/building/REAL300000220013 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220013 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220013/0 /scratch/stefan/7769801/working/building/REAL300000220013 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/13 `/scratch/stefan/7769801/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)C(=O)NC2=C1) `REAL300000220013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220013 none N#CC1=CC=C2C(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 11, 11, 1, 1, 1, 6, 6, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 6, 6, 3, 6, 6, 7, 7] 33 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220013 none N#CC1=CC=C2C(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 20, 20, 20, 6, 6, 6, 6, 6, 21, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 6, 21, 21, 1, 1, 1, 1, 1, 20, 20] 33 rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 115 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220013 none N#CC1=CC=C2C(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 7, 7, 7, 26, 28, 28, 7, 7, 7, 20, 20, 8, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 7, 26, 26, 20, 20, 11, 20, 20, 1, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 23, 24, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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 /scratch/stefan/7769801/working/building/REAL300000220013 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220013 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220013/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220013 Building REAL300000220014 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220014' /scratch/stefan/7769801/working/building/REAL300000220014 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220014 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220014/0 /scratch/stefan/7769801/working/building/REAL300000220014 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/14 `/scratch/stefan/7769801/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)C(=O)NC2=C1) `REAL300000220014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220014 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 19, 19, 11, 11, 11, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 11, 11, 22, 11, 9, 9] 80 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220014 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [40, 40, 40, 40, 40, 40, 40, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 40, 40, 40, 40, 40, 40, 40, 40, 11, 11, 1, 1, 2, 1, 40, 40] 80 rigid atoms, others: [33, 34, 36, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 37, 38]) total number of confs: 96 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220014 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 40, 40, 80, 40, 1, 1] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 23, 24, 25, 26, 27, 28, 29, 30, 37] set([32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220014 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220014 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220014/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220014 Building REAL300000220015 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220015' /scratch/stefan/7769801/working/building/REAL300000220015 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220015 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220015/0 /scratch/stefan/7769801/working/building/REAL300000220015 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/15 `/scratch/stefan/7769801/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)C(=O)NC2=C1) `REAL300000220015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220015 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 2, 3, 3, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1, 3, 3] 3 rigid atoms, others: [32, 37, 38, 7, 8, 9, 10, 11, 12, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39, 40]) total number of confs: 15 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220015 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3] 3 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 18 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220015 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 23, 24, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 9 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220015 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220015 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220015/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220015 Building REAL300000220016 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220016' /scratch/stefan/7769801/working/building/REAL300000220016 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220016 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220016/0 /scratch/stefan/7769801/working/building/REAL300000220016 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/16 `/scratch/stefan/7769801/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CNC4=CC=C(C(=O)[O-])C=C34)C(=O)NC2=C1) `REAL300000220016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220016 none N#CC1=CC=C2C(=CC3=CNC4=CC=C(C(=O)[O-])C=C34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4] 4 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 34, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 9 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220016 none N#CC1=CC=C2C(=CC3=CNC4=CC=C(C(=O)[O-])C=C34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 20, 21, 22, 23, 24, 25, 26, 27] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31]) total number of confs: 5 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220016 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220016 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220016/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220016 Building REAL300000220017 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220017' /scratch/stefan/7769801/working/building/REAL300000220017 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220017 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220017/0 /scratch/stefan/7769801/working/building/REAL300000220017 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/17 `/scratch/stefan/7769801/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C32)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000220017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220017 none COC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C32)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [18, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 24, 47, 47, 48, 48, 18, 18, 18, 7, 1, 1, 1, 1, 1, 7, 47, 47, 47, 47] 48 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 36] set([0, 1, 2, 3, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41]) 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: REAL300000220017 none COC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C32)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 18, 18, 26, 26, 3, 3, 3, 1, 7, 7, 7, 7, 7, 1, 18, 18, 18, 18] 48 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 37, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220017 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220017 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220017/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220017 Building REAL300000220018 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220018' /scratch/stefan/7769801/working/building/REAL300000220018 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220018 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220018/0 /scratch/stefan/7769801/working/building/REAL300000220018 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/18 `/scratch/stefan/7769801/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C(O)=C3)C(=O)NC2=C1) `REAL300000220018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220018 none N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C(O)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 1, 3, 3] 6 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 26, 27, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 28, 30, 31]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220018 none N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C(O)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 3, 1, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220018 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220018 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220018/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220018 Building REAL300000220019 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220019' /scratch/stefan/7769801/working/building/REAL300000220019 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220019 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220019/0 /scratch/stefan/7769801/working/building/REAL300000220019 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/19 `/scratch/stefan/7769801/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=C2C(=O)NC3=CC(C#N)=CC=C23)C=C1C(=O)[O-]) `REAL300000220019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220019 none CC1=CC=C(C=C2C(=O)NC3=CC(C#N)=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7] 7 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 33, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220019 none CC1=CC=C(C=C2C(=O)NC3=CC(C#N)=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 18, 19, 20, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220019 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220019 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220019/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220019 Building REAL300000220020 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220020' /scratch/stefan/7769801/working/building/REAL300000220020 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220020 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220020/0 /scratch/stefan/7769801/working/building/REAL300000220020 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/20 `/scratch/stefan/7769801/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=C(Cl)S3)C(=O)NC2=C1) `REAL300000220020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220020 none N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=C(Cl)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7] 7 rigid atoms, others: [7, 8, 9, 10, 11, 14, 15, 16, 25] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27]) 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: REAL300000220020 none N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=C(Cl)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 1, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 25]) total number of confs: 8 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220020 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220020 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220020/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220020 Building REAL300000220021 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220021' /scratch/stefan/7769801/working/building/REAL300000220021 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220021 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220021/0 /scratch/stefan/7769801/working/building/REAL300000220021 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/21 `/scratch/stefan/7769801/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)C(=O)NC2=C1) `REAL300000220021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220021 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 2, 3, 5, 5, 5, 5, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 5, 5, 5, 5, 4, 4] 9 rigid atoms, others: [7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220021 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 1, 1, 1, 1, 9, 9] 9 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 24 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220021 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 9, 4, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 1, 1] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 37, 22, 23, 24, 25, 26, 27, 28, 29, 36] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220021 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220021 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220021/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220021 Building REAL300000220022 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220022' /scratch/stefan/7769801/working/building/REAL300000220022 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220022 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220022/0 /scratch/stefan/7769801/working/building/REAL300000220022 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/22 `/scratch/stefan/7769801/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)C(=O)NC2=C1) `REAL300000220022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220022 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 6, 4, 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: [8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 11, 11, 22, 11, 8, 8] 54 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220022 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 6, 4, 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: [27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 1, 1, 2, 1, 27, 27] 54 rigid atoms, others: [33, 34, 36, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 37, 38]) total number of confs: 66 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220022 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 27, 54, 27, 1, 1] 54 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 23, 24, 25, 26, 27, 28, 29, 30, 37] set([32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220022 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220022 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220022/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220022 Building REAL300000220023 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220023' /scratch/stefan/7769801/working/building/REAL300000220023 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220023 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220023/0 /scratch/stefan/7769801/working/building/REAL300000220023 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/23 `/scratch/stefan/7769801/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)C(=O)NC2=C1) `REAL300000220023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220023 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 11, 11, 11, 11, 7, 7] 19 rigid atoms, others: [7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 26 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220023 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 1, 1, 1, 1, 19, 19] 19 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 44 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220023 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 37, 22, 23, 24, 25, 26, 27, 28, 29, 36] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220023 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220023 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220023/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220023 Building REAL300000220024 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220024' /scratch/stefan/7769801/working/building/REAL300000220024 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220024 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220024/0 /scratch/stefan/7769801/working/building/REAL300000220024 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/24 `/scratch/stefan/7769801/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=C1C(=O)NC2=CC(C#N)=CC=C12) `REAL300000220024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220024 none COC1=CC=C(C(=O)[O-])C=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1] 5 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28, 29]) total number of confs: 6 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220024 none COC1=CC=C(C(=O)[O-])C=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5] 5 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 27, 28, 29] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220024 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220024 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220024/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220024 Building REAL300000220025 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220025' /scratch/stefan/7769801/working/building/REAL300000220025 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220025 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220025/0 /scratch/stefan/7769801/working/building/REAL300000220025 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/25 `/scratch/stefan/7769801/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CSC4=CC=C(C(=O)[O-])C=C34)C(=O)NC2=C1) `REAL300000220025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220025 none N#CC1=CC=C2C(=CC3=CSC4=CC=C(C(=O)[O-])C=C34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220025 none N#CC1=CC=C2C(=CC3=CSC4=CC=C(C(=O)[O-])C=C34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220025 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220025 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220025/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220025 Building REAL300000220026 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220026' /scratch/stefan/7769801/working/building/REAL300000220026 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220026 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220026/0 /scratch/stefan/7769801/working/building/REAL300000220026 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/26 `/scratch/stefan/7769801/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=CC=C3Br)C(=O)NC2=C1) `REAL300000220026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220026 none N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=CC=C3Br)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220026 none N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=CC=C3Br)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220026 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220026 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220026/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220026 Building REAL300000220027 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220027' /scratch/stefan/7769801/working/building/REAL300000220027 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220027 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220027/0 /scratch/stefan/7769801/working/building/REAL300000220027 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/27 `/scratch/stefan/7769801/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C=C3[N+](=O)[O-])C(=O)NC2=C1) `REAL300000220027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220027 none N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C=C3[N+](=O)[O-])C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220027 none N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C=C3[N+](=O)[O-])C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 25, 26, 27, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220027 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220027 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220027/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220027 Building REAL300000220028 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220028' /scratch/stefan/7769801/working/building/REAL300000220028 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220028 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220028/0 /scratch/stefan/7769801/working/building/REAL300000220028 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/28 `/scratch/stefan/7769801/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=CC(CC(=O)[O-])=C1) `REAL300000220028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220028 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=CC(CC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 4, 4, 4, 4, 4, 1, 1, 1, 3, 3, 1] 6 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18, 22, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32]) total number of confs: 18 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220028 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=CC(CC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 4, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 4] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27] set([32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220028 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220028 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220028/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220028 Building REAL300000220029 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220029' /scratch/stefan/7769801/working/building/REAL300000220029 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220029 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220029/0 /scratch/stefan/7769801/working/building/REAL300000220029 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/29 `/scratch/stefan/7769801/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C23)=CC=C1C(=O)[O-]) `REAL300000220029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220029 none COC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C23)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 5, 5] 7 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 33, 34, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 18 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220029 none COC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C23)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 5, 5, 5, 5, 5, 1, 1] 7 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 18, 19, 20, 21, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220029 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220029 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220029/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220029 Building REAL300000220030 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220030' /scratch/stefan/7769801/working/building/REAL300000220030 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220030 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220030/0 /scratch/stefan/7769801/working/building/REAL300000220030 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/30 `/scratch/stefan/7769801/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=C(F)C=C(C(=O)[O-])C=C3F)C(=O)NC2=C1) `REAL300000220030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220030 none N#CC1=CC=C2C(=CC3=C(F)C=C(C(=O)[O-])C=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2] 2 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 9 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220030 none N#CC1=CC=C2C(=CC3=C(F)C=C(C(=O)[O-])C=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1] 2 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220030 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220030 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220030/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220030 Building REAL300000220031 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220031' /scratch/stefan/7769801/working/building/REAL300000220031 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220031 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220031/0 /scratch/stefan/7769801/working/building/REAL300000220031 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/31 `/scratch/stefan/7769801/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=C(F)C=CC(C(=O)[O-])=C3F)C(=O)NC2=C1) `REAL300000220031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220031 none N#CC1=CC=C2C(=CC3=C(F)C=CC(C(=O)[O-])=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 7, 7] 7 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) 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: REAL300000220031 none N#CC1=CC=C2C(=CC3=C(F)C=CC(C(=O)[O-])=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28]) total number of confs: 8 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220031 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220031 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220031/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220031 Building REAL300000220032 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220032' /scratch/stefan/7769801/working/building/REAL300000220032 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220032 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220032/0 /scratch/stefan/7769801/working/building/REAL300000220032 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/32 `/scratch/stefan/7769801/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1) `REAL300000220032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220032 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 5, 1, 1, 2, 2, 2, 2, 2, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1] 9 rigid atoms, others: [34, 35, 42, 43, 12, 13, 14, 15, 16, 17, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220032 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 5, 5, 5, 5, 5, 5, 3, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 3, 1, 5, 5] 9 rigid atoms, others: [36, 37, 38, 41, 16, 17, 18, 19, 20, 21, 22, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 42, 43]) total number of confs: 30 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220032 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 5, 5, 9, 9, 9, 5, 2, 2, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 9, 9, 5, 2, 2] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 33, 29, 30, 31] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220032 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220032 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220032/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220032 Building REAL300000220033 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220033' /scratch/stefan/7769801/working/building/REAL300000220033 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220033 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220033/0 /scratch/stefan/7769801/working/building/REAL300000220033 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/33 `/scratch/stefan/7769801/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C23)=CC=C1OCC(=O)[O-]) `REAL300000220033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220033 none CCOC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C23)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 36, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 53, 143, 167, 167, 109, 109, 109, 109, 109, 7, 1, 1, 1, 1, 1, 7, 7, 143, 143] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 37] set([0, 1, 2, 3, 4, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41]) total number of confs: 870 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: REAL300000220033 none CCOC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C23)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 9, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 9, 47, 88, 88, 41, 41, 41, 41, 41, 1, 7, 7, 7, 7, 7, 1, 1, 47, 47] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 19, 20, 21, 22, 38] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 423 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220033 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220033 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220033/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220033 Building REAL300000220034 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220034' /scratch/stefan/7769801/working/building/REAL300000220034 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220034 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220034/0 /scratch/stefan/7769801/working/building/REAL300000220034 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/34 `/scratch/stefan/7769801/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC(F)=C(C(=O)[O-])C(F)=C3)C(=O)NC2=C1) `REAL300000220034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220034 none N#CC1=CC=C2C(=CC3=CC(F)=C(C(=O)[O-])C(F)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2] 2 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 9 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220034 none N#CC1=CC=C2C(=CC3=CC(F)=C(C(=O)[O-])C(F)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1] 2 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28]) total number of confs: 3 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220034 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220034 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220034/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220034 Building REAL300000220035 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220035' /scratch/stefan/7769801/working/building/REAL300000220035 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220035 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220035/0 /scratch/stefan/7769801/working/building/REAL300000220035 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/35 `/scratch/stefan/7769801/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC4=C(C=C(C(=O)[O-])N4)O3)C(=O)NC2=C1) `REAL300000220035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220035 none N#CC1=CC=C2C(=CC3=CC4=C(C=C(C(=O)[O-])N4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5] 5 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220035 none N#CC1=CC=C2C(=CC3=CC4=C(C=C(C(=O)[O-])N4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29]) total number of confs: 6 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220035 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220035 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220035/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220035 Building REAL300000220036 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220036' /scratch/stefan/7769801/working/building/REAL300000220036 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220036 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220036/0 /scratch/stefan/7769801/working/building/REAL300000220036 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/36 `/scratch/stefan/7769801/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C4OC(C(=O)[O-])=CC4=C3)C(=O)NC2=C1) `REAL300000220036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220036 none N#CC1=CC=C2C(=CC3=CC=C4OC(C(=O)[O-])=CC4=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 15, 16, 33, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220036 none N#CC1=CC=C2C(=CC3=CC=C4OC(C(=O)[O-])=CC4=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220036 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220036 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220036/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220036 Building REAL300000220037 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220037' /scratch/stefan/7769801/working/building/REAL300000220037 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220037 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220037/0 /scratch/stefan/7769801/working/building/REAL300000220037 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/37 `/scratch/stefan/7769801/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=CN4C(C(=O)[O-])=CN=C34)C(=O)NC2=C1) `REAL300000220037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220037 none N#CC1=CC=C2C(=CC3=CC=CN4C(C(=O)[O-])=CN=C34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 15, 16, 33, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220037 none N#CC1=CC=C2C(=CC3=CC=CN4C(C(=O)[O-])=CN=C34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220037 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220037 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220037/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220037 Building REAL300000220038 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220038' /scratch/stefan/7769801/working/building/REAL300000220038 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220038 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220038/0 /scratch/stefan/7769801/working/building/REAL300000220038 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/38 `/scratch/stefan/7769801/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=C1C(=O)NC2=CC(C#N)=CC=C12) `REAL300000220038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220038 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 3 rigid atoms, others: [34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220038 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220038 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220038 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220038/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220038 Building REAL300000220039 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220039' /scratch/stefan/7769801/working/building/REAL300000220039 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220039 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220039/0 /scratch/stefan/7769801/working/building/REAL300000220039 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/39 `/scratch/stefan/7769801/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CN=C4C=CC(C(=O)[O-])=CN34)C(=O)NC2=C1) `REAL300000220039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220039 none N#CC1=CC=C2C(=CC3=CN=C4C=CC(C(=O)[O-])=CN34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4] 4 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 33, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220039 none N#CC1=CC=C2C(=CC3=CN=C4C=CC(C(=O)[O-])=CN34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31]) total number of confs: 5 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220039 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220039 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220039/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220039 Building REAL300000220040 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220040' /scratch/stefan/7769801/working/building/REAL300000220040 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220040 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220040/0 /scratch/stefan/7769801/working/building/REAL300000220040 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/40 `/scratch/stefan/7769801/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)C(=O)NC2=C1) `REAL300000220040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220040 none N#CC1=CC=C2C(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 7, 7, 1, 1, 4, 4] 7 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37]) total number of confs: 16 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220040 none N#CC1=CC=C2C(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 7, 7, 7, 7] 7 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 30 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220040 none N#CC1=CC=C2C(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 4, 4, 1, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 37, 22, 23, 24, 25, 26, 27, 28, 29, 36] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220040 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220040 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220040/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220040 Building REAL300000220041 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220041' /scratch/stefan/7769801/working/building/REAL300000220041 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220041 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220041/0 /scratch/stefan/7769801/working/building/REAL300000220041 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/41 `/scratch/stefan/7769801/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=CC(C(=O)[O-])=C3F)C(=O)NC2=C1) `REAL300000220041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220041 none N#CC1=CC=C2C(=CC3=CC=CC(C(=O)[O-])=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7] 7 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) 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: REAL300000220041 none N#CC1=CC=C2C(=CC3=CC=CC(C(=O)[O-])=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28]) total number of confs: 8 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220041 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220041 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220041/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220041 Building REAL300000220042 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220042' /scratch/stefan/7769801/working/building/REAL300000220042 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220042 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220042/0 /scratch/stefan/7769801/working/building/REAL300000220042 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/42 `/scratch/stefan/7769801/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(OCC(=O)[O-])C(Cl)=C3)C(=O)NC2=C1) `REAL300000220042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220042 none N#CC1=CC=C2C(=CC3=CC=C(OCC(=O)[O-])C(Cl)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 36, 42, 42, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 36, 36, 1, 7, 7] 49 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33, 34]) total number of confs: 154 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: REAL300000220042 none N#CC1=CC=C2C(=CC3=CC=C(OCC(=O)[O-])C(Cl)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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, 1, 1, 1, 1, 1, 1, 7, 7, 4, 7, 28, 49, 49, 49, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 49, 49, 7, 1, 1] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 20, 21, 22, 23, 24, 25, 26, 27] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220042 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220042 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220042/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220042 Building REAL300000220043 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220043' /scratch/stefan/7769801/working/building/REAL300000220043 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220043 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220043/0 /scratch/stefan/7769801/working/building/REAL300000220043 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/43 `/scratch/stefan/7769801/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(S(=O)(=O)NCC(=O)[O-])C=C3)C(=O)NC2=C1) `REAL300000220043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220043 none N#CC1=CC=C2C(=CC3=CC=C(S(=O)(=O)NCC(=O)[O-])C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 32, 34, 34, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 9, 32, 32, 1, 1, 4, 4] 35 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38]) 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: REAL300000220043 none N#CC1=CC=C2C(=CC3=CC=C(S(=O)(=O)NCC(=O)[O-])C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 20, 35, 35, 35, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 20, 35, 35, 4, 4, 1, 1] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 22, 23, 24, 25, 26, 27, 28, 29, 37] set([32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220043 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220043 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220043/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220043 Building REAL300000220044 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220044' /scratch/stefan/7769801/working/building/REAL300000220044 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220044 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220044/0 /scratch/stefan/7769801/working/building/REAL300000220044 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/44 `/scratch/stefan/7769801/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)C(=O)NC2=C1) `REAL300000220044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220044 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 8, 8, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 7, 7, 6, 7, 1, 1, 4, 4] 8 rigid atoms, others: [32, 37, 38, 7, 8, 9, 10, 11, 12, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39, 40]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220044 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 7, 7, 8, 8] 8 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 38 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220044 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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, 1, 1, 1, 4, 4, 1, 1, 8, 8, 7, 8, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 4, 4, 1, 1] 8 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 39, 23, 24, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220044 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220044 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220044/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220044 Building REAL300000220045 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220045' /scratch/stefan/7769801/working/building/REAL300000220045 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220045 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220045/0 /scratch/stefan/7769801/working/building/REAL300000220045 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/45 `/scratch/stefan/7769801/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=C1C(=O)NC2=CC(C#N)=CC=C12) `REAL300000220045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220045 none COC1=CC(C(=O)[O-])=CC=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1] 5 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28, 29]) total number of confs: 6 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220045 none COC1=CC(C(=O)[O-])=CC=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 1, 1, 1, 5, 5, 5, 5, 5] 5 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 27, 28, 29] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 18 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220045 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220045 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220045/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220045 Building REAL300000220046 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220046' /scratch/stefan/7769801/working/building/REAL300000220046 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220046 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220046/0 /scratch/stefan/7769801/working/building/REAL300000220046 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/46 `/scratch/stefan/7769801/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=C4C=C(C(=O)[O-])SC4=CC=C3F)C(=O)NC2=C1) `REAL300000220046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220046 none N#CC1=CC=C2C(=CC3=C4C=C(C(=O)[O-])SC4=CC=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 33, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220046 none N#CC1=CC=C2C(=CC3=C4C=C(C(=O)[O-])SC4=CC=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 21, 22, 23, 24, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220046 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220046 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220046/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220046 Building REAL300000220047 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220047' /scratch/stefan/7769801/working/building/REAL300000220047 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220047 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220047/0 /scratch/stefan/7769801/working/building/REAL300000220047 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/47 `/scratch/stefan/7769801/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C(F)=C2)N1) `REAL300000220047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220047 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [25, 25, 25, 25, 38, 42, 42, 25, 25, 25, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 25, 25, 25, 25, 38, 38, 5, 5, 1, 1, 5, 5, 1, 25] 56 rigid atoms, others: [33, 34, 37, 12, 13, 14, 15, 16, 17, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38]) total number of confs: 134 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220047 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [42, 42, 42, 42, 56, 56, 56, 42, 42, 42, 14, 14, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 42, 42, 42, 42, 56, 56, 14, 14, 5, 5, 1, 1, 5, 42] 56 rigid atoms, others: [35, 36, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 167 number of broken/clashed sets: 56 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220047 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 25, 42, 42, 42, 42, 25, 25, 25, 1, 2, 2, 2, 3, 3, 11, 11, 25, 25, 42, 42, 25, 1] 56 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 25] set([4, 5, 6, 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: 99 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220047 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220047 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220047/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220047 Building REAL300000220048 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220048' /scratch/stefan/7769801/working/building/REAL300000220048 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220048 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220048/0 /scratch/stefan/7769801/working/building/REAL300000220048 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/48 `/scratch/stefan/7769801/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=C(Cl)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220048 none CCCOC1=C(Cl)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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, 12, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 79, 59, 31, 31, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 31, 31, 31, 71, 138, 138, 138, 138, 138, 79, 79, 31, 9, 9, 2, 2, 2, 3, 3, 1, 31, 71, 71, 71] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 647 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220048 none CCCOC1=C(Cl)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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, 12, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 31, 31, 31, 31, 31, 58, 101, 101, 31, 31, 31, 1, 1, 1, 3, 15, 15, 15, 14, 14, 8, 8, 1, 5, 5, 31, 31, 31, 58, 58, 31, 1, 4, 4, 4] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 43, 23, 24, 25] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 456 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220048 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220048 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220048/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220048 Building REAL300000220049 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220049' /scratch/stefan/7769801/working/building/REAL300000220049 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220049 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220049/0 /scratch/stefan/7769801/working/building/REAL300000220049 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/49 `/scratch/stefan/7769801/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)O2)N1) `REAL300000220049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220049 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 75, 87, 87, 51, 52, 51, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 12, 1, 52, 52, 52, 52, 75, 75, 12, 12, 1, 1, 12, 12, 10, 12, 52] 201 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 300 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220049 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 201, 201, 201, 165, 165, 165, 67, 67, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 165, 165, 165, 165, 201, 201, 67, 67, 12, 12, 1, 1, 1, 1, 165] 201 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 505 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220049 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 52, 52, 52, 52, 165, 165, 72, 165, 165, 165, 52, 1, 2, 2, 2, 3, 3, 11, 11, 52, 52, 165, 165, 165, 165, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 39] set([4, 5, 6, 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: 553 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220049 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220049 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220049/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220049 Building REAL300000220050 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220050' /scratch/stefan/7769801/working/building/REAL300000220050 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220050 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220050/0 /scratch/stefan/7769801/working/building/REAL300000220050 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/50 `/scratch/stefan/7769801/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC(F)F) `REAL300000220050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220050 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 31, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 31, 31, 31, 94, 145, 145, 85, 85, 85, 31, 31, 9, 9, 2, 2, 2, 3, 3, 1, 31, 145] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 534 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220050 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 31, 31, 31, 31, 31, 57, 95, 95, 31, 31, 31, 1, 1, 1, 7, 15, 15, 4, 4, 4, 1, 1, 5, 5, 31, 31, 31, 57, 57, 31, 1, 15] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 20, 21, 22, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 401 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220050 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220050 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220050/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220050 Building REAL300000220051 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220051' /scratch/stefan/7769801/working/building/REAL300000220051 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220051 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220051/0 /scratch/stefan/7769801/working/building/REAL300000220051 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/51 `/scratch/stefan/7769801/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(Cl)C=C3)=N2)=N1) `REAL300000220051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220051 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(Cl)C=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [45, 44, 45, 45, 68, 68, 68, 45, 45, 45, 12, 12, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 3, 1, 44, 45, 45, 45, 68, 68, 41, 12, 12, 1, 3, 3, 3, 3] 68 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 220 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220051 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(Cl)C=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [54, 54, 54, 54, 68, 68, 68, 54, 54, 54, 23, 23, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 54, 54, 54, 54, 68, 68, 53, 23, 23, 3, 1, 1, 1, 1] 68 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 179 number of broken/clashed sets: 67 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220051 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(Cl)C=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 45, 45, 45, 45, 54, 54, 53, 54, 54, 54, 45, 1, 2, 2, 2, 3, 3, 1, 11, 11, 45, 54, 54, 54, 54] 68 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 114 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220051 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220051 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220051/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220051 Building REAL300000220052 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220052' /scratch/stefan/7769801/working/building/REAL300000220052 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220052 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220052/0 /scratch/stefan/7769801/working/building/REAL300000220052 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/52 `/scratch/stefan/7769801/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)=C1) `REAL300000220052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220052 none COC1=CC=CC(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 12, 12, 63, 63, 64, 64, 64, 98, 141, 141, 64, 64, 64, 1, 1, 4, 9, 9, 9, 4, 4, 4, 12, 12, 64, 64, 64, 98, 98, 60, 1, 4] 201 rigid atoms, others: [6, 7, 8, 9, 10, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 483 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220052 none COC1=CC=CC(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 133, 133, 133, 133, 133, 64, 64, 64, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 64, 64, 133, 163, 163, 163, 133, 133, 133, 12, 12, 2, 2, 2, 3, 3, 1, 64, 133] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 278 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220052 none COC1=CC=CC(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 37, 37, 133, 133, 133, 133, 133, 171, 201, 201, 133, 133, 133, 4, 4, 1, 3, 3, 3, 1, 1, 1, 37, 37, 133, 133, 133, 171, 171, 130, 4, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 42, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 552 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220052 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220052 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220052/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220052 Building REAL300000220053 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220053' /scratch/stefan/7769801/working/building/REAL300000220053 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220053 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220053/0 /scratch/stefan/7769801/working/building/REAL300000220053 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/53 `/scratch/stefan/7769801/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC(F)F) `REAL300000220053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220053 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 67, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 27, 27, 27, 27, 113, 166, 166, 68, 68, 68, 68, 68, 27, 9, 9, 2, 2, 2, 3, 3, 1, 27, 27, 166] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 530 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220053 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 5, 1, 1, 1, 1, 1, 5, 5, 27, 27, 27, 27, 27, 48, 83, 83, 27, 27, 27, 1, 1, 1, 1, 9, 25, 25, 6, 6, 6, 6, 6, 1, 5, 5, 27, 27, 27, 48, 48, 27, 1, 1, 25] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 41, 42, 20, 21, 22, 23] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 387 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220053 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220053 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220053/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220053 Building REAL300000220054 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220054' /scratch/stefan/7769801/working/building/REAL300000220054 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220054 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220054/0 /scratch/stefan/7769801/working/building/REAL300000220054 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/54 `/scratch/stefan/7769801/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(C)=C1OC(F)F) `REAL300000220054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220054 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(C)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 1, 12, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 35, 35, 35, 21, 33, 51, 88, 88, 35, 35, 35, 35, 11, 11, 2, 2, 2, 3, 3, 1, 35, 35, 35, 35, 88] 102 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 384 number of broken/clashed sets: 102 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220054 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(C)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 1, 12, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 35, 35, 35, 35, 35, 51, 69, 69, 35, 35, 35, 1, 1, 1, 1, 1, 2, 16, 16, 2, 2, 2, 1, 5, 5, 35, 35, 35, 51, 51, 35, 1, 2, 2, 2, 16] 102 rigid atoms, others: [0, 1, 2, 3, 4, 38, 18, 19, 20, 21, 22, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 275 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220054 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220054 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220054/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220054 Building REAL300000220055 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220055' /scratch/stefan/7769801/working/building/REAL300000220055 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220055 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220055/0 /scratch/stefan/7769801/working/building/REAL300000220055 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/55 `/scratch/stefan/7769801/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC2=C(C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1)OC(C)C2) `REAL300000220055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220055 none CCOC1=CC2=C(C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1)OC(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 140, 72, 72, 72, 72, 72, 72, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 72, 72, 72, 72, 169, 169, 169, 169, 169, 72, 72, 12, 12, 2, 2, 2, 3, 3, 1, 72, 72, 72, 72, 72, 72] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 391 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220055 none CCOC1=CC2=C(C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1)OC(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 72, 72, 72, 72, 72, 119, 162, 162, 72, 72, 72, 1, 1, 1, 1, 29, 29, 29, 29, 29, 1, 1, 9, 9, 72, 72, 72, 119, 119, 72, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 42, 46, 47, 23, 24, 25, 26] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 636 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220055 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220055 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220055/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220055 Building REAL300000220056 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220056' /scratch/stefan/7769801/working/building/REAL300000220056 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220056 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220056/0 /scratch/stefan/7769801/working/building/REAL300000220056 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/56 `/scratch/stefan/7769801/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=NC4=CC=CC=C4S3)O2)=N1) `REAL300000220056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220056 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=NC4=CC=CC=C4S3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 70, 70, 104, 130, 130, 71, 71, 71, 12, 12, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 1, 71, 71, 71, 71, 104, 104, 71, 13, 12, 1, 1, 13, 13, 12, 13] 201 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 418 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220056 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=NC4=CC=CC=C4S3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 201, 201, 201, 167, 167, 167, 53, 53, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 167, 167, 167, 167, 201, 201, 167, 53, 53, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 466 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220056 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=NC4=CC=CC=C4S3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 71, 71, 71, 71, 167, 167, 167, 167, 167, 167, 167, 167, 70, 1, 2, 2, 2, 3, 3, 1, 12, 12, 71, 71, 167, 167, 167, 167] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 253 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220056 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220056 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220056/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220056 Building REAL300000220057 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220057' /scratch/stefan/7769801/working/building/REAL300000220057 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220057 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220057/0 /scratch/stefan/7769801/working/building/REAL300000220057 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/57 `/scratch/stefan/7769801/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN1N=C(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Cl) `REAL300000220057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220057 none CCCCN1N=C(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'Cl', 'H', 'H', 'H', 'H', '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, 8, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 126, 41, 41, 41, 41, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 41, 41, 147, 147, 147, 147, 147, 147, 147, 126, 126, 41, 41, 41, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [44, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 559 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220057 none CCCCN1N=C(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'Cl', 'H', 'H', 'H', 'H', '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, 8, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 41, 41, 67, 96, 96, 41, 41, 41, 1, 1, 9, 9, 9, 9, 9, 9, 9, 5, 5, 2, 2, 2, 7, 7, 41, 41, 41, 67, 67, 41] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 24] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 372 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220057 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220057 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220057/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220057 Building REAL300000220058 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220058' /scratch/stefan/7769801/working/building/REAL300000220058 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220058 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220058/0 /scratch/stefan/7769801/working/building/REAL300000220058 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/58 `/scratch/stefan/7769801/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C) `REAL300000220058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220058 none CC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 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: [12, 11, 24, 24, 24, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 3, 3, 2, 2, 2, 1, 24, 24, 24, 24] 37 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 164 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: REAL300000220058 none CC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 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, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 24, 37, 37, 37, 24, 24, 24, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 9, 9, 37, 37, 24, 24, 24, 23, 1, 2, 2, 2] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 26, 38] set([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, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220058 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220058 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220058/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220058 Building REAL300000220059 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220059' /scratch/stefan/7769801/working/building/REAL300000220059 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220059 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220059/0 /scratch/stefan/7769801/working/building/REAL300000220059 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/59 `/scratch/stefan/7769801/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(=O)[O-]) `REAL300000220059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220059 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 26, 26, 26, 26, 116, 138, 157, 157, 47, 47, 47, 26, 8, 8, 2, 2, 2, 3, 3, 1, 26, 26, 138, 138] 201 rigid atoms, others: [38, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 424 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220059 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 26, 26, 26, 26, 26, 49, 83, 83, 26, 26, 26, 1, 1, 1, 1, 7, 20, 33, 33, 3, 3, 3, 1, 5, 5, 26, 26, 26, 49, 49, 26, 1, 1, 20, 20] 201 rigid atoms, others: [1, 2, 3, 4, 5, 39, 40, 19, 20, 21, 22, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 419 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220059 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220059 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220059/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220059 Building REAL300000220060 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220060' /scratch/stefan/7769801/working/building/REAL300000220060 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220060 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220060/0 /scratch/stefan/7769801/working/building/REAL300000220060 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/60 `/scratch/stefan/7769801/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=C(C)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220060 none CC1=NN(CC2=CC=C(C)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 10, 9, 9, 39, 39, 140, 140, 140, 140, 140, 201, 201, 201, 140, 140, 140, 10, 10, 10, 3, 3, 1, 1, 2, 2, 2, 1, 1, 10, 10, 10, 39, 39, 140, 140, 140, 201, 201, 140] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 40, 39] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 606 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220060 none CC1=NN(CC2=CC=C(C)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 45, 45, 45, 128, 140, 140, 132, 132, 140, 140, 45, 45, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 45, 45, 45, 128, 128, 140, 140, 140, 140, 140, 140, 140, 45, 45, 45, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [51, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 564 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220060 none CC1=NN(CC2=CC=C(C)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 10, 10, 8, 8, 10, 10, 1, 1, 1, 1, 7, 7, 45, 45, 45, 45, 45, 80, 90, 90, 45, 45, 45, 2, 2, 2, 5, 5, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 7, 7, 45, 45, 45, 80, 80, 45] 201 rigid atoms, others: [0, 1, 2, 3, 4, 12, 13, 14, 15] set([5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 363 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220060 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220060 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220060/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220060 Building REAL300000220061 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220061' /scratch/stefan/7769801/working/building/REAL300000220061 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220061 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220061/0 /scratch/stefan/7769801/working/building/REAL300000220061 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/61 `/scratch/stefan/7769801/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1O) `REAL300000220061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220061 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [59, 37, 37, 37, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 37, 37, 37, 37, 37, 59, 59, 59, 37, 11, 11, 2, 2, 2, 3, 3, 1, 37, 74] 152 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 197 number of broken/clashed sets: 152 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220061 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 1, 1, 1, 1, 5, 5, 37, 37, 37, 37, 37, 61, 76, 76, 37, 37, 37, 1, 1, 1, 1, 1, 4, 4, 4, 1, 5, 5, 37, 37, 37, 61, 61, 37, 1, 2] 152 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 36, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 262 number of broken/clashed sets: 152 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220061 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220061 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220061/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220061 Building REAL300000220062 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220062' /scratch/stefan/7769801/working/building/REAL300000220062 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220062 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220062/0 /scratch/stefan/7769801/working/building/REAL300000220062 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/62 `/scratch/stefan/7769801/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(Br)=C2)=N1) `REAL300000220062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220062 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 20, 20, 20, 32, 32, 32, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 32, 32, 20, 7, 7, 1, 1, 1] 32 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 106 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: REAL300000220062 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 7, 7, 1, 1, 1, 1, 1, 8, 8, 20, 20, 15, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 1, 8, 8, 20, 20, 20] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 88 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220062 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220062 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220062/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220062 Building REAL300000220063 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220063' /scratch/stefan/7769801/working/building/REAL300000220063 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220063 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220063/0 /scratch/stefan/7769801/working/building/REAL300000220063 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/63 `/scratch/stefan/7769801/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1O) `REAL300000220063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220063 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [172, 140, 53, 53, 53, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 53, 53, 53, 53, 53, 172, 172, 172, 172, 172, 53, 12, 12, 2, 2, 2, 3, 3, 1, 53, 106] 402 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 520 number of broken/clashed sets: 402 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220063 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 1, 1, 1, 1, 1, 7, 7, 53, 53, 53, 53, 53, 94, 132, 132, 53, 53, 53, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 1, 7, 7, 53, 53, 53, 94, 94, 53, 1, 2] 402 rigid atoms, others: [2, 3, 4, 5, 6, 39, 20, 21, 22, 23, 24, 30] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 540 number of broken/clashed sets: 402 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220063 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220063 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220063/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220063 Building REAL300000220064 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220064' /scratch/stefan/7769801/working/building/REAL300000220064 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220064 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220064/0 /scratch/stefan/7769801/working/building/REAL300000220064 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/64 `/scratch/stefan/7769801/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC#N)N1) `REAL300000220064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220064 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC#N)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 99, 151, 151, 58, 58, 58, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 8, 34, 34, 58, 58, 58, 58, 99, 99, 9, 9, 1, 1, 1, 1, 34, 34, 58] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 620 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220064 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC#N)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 58, 58, 23, 58, 58, 58, 106, 169, 169, 1, 2, 2, 2, 3, 3, 11, 11, 58, 58, 58, 58, 169, 169, 1] 201 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 588 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220064 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220064 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220064/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220064 Building REAL300000220065 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220065' /scratch/stefan/7769801/working/building/REAL300000220065 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220065 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220065/0 /scratch/stefan/7769801/working/building/REAL300000220065 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/65 `/scratch/stefan/7769801/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1OC) `REAL300000220065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220065 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [77, 39, 39, 39, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 39, 39, 39, 39, 39, 83, 77, 77, 77, 39, 12, 12, 2, 2, 2, 3, 3, 1, 39, 83, 83, 83] 118 rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 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: 221 number of broken/clashed sets: 118 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220065 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 39, 39, 39, 39, 39, 65, 82, 82, 39, 39, 39, 1, 1, 1, 1, 1, 6, 4, 4, 4, 1, 5, 5, 39, 39, 39, 65, 65, 39, 1, 7, 7, 7] 118 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 28, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 294 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220065 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220065 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220065/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220065 Building REAL300000220066 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220066' /scratch/stefan/7769801/working/building/REAL300000220066 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220066 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220066/0 /scratch/stefan/7769801/working/building/REAL300000220066 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/66 `/scratch/stefan/7769801/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(O)C(Br)=C2)=N1) `REAL300000220066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220066 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(O)C(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 32, 32, 32, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 32, 32, 20, 7, 7, 1, 1, 2, 1] 64 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 108 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220066 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(O)C(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 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 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, 1, 3, 6, 6, 1, 1, 1, 1, 1, 8, 8, 20, 20, 15, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 1, 8, 8, 20, 20, 40, 20] 64 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 126 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220066 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220066 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220066/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220066 Building REAL300000220067 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220067' /scratch/stefan/7769801/working/building/REAL300000220067 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220067 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220067/0 /scratch/stefan/7769801/working/building/REAL300000220067 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/67 `/scratch/stefan/7769801/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC(C)C) `REAL300000220067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220067 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 75, 98, 129, 129, 39, 39, 39, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 98, 98, 129, 129, 129, 129, 129, 129, 129] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 489 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220067 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 39, 70, 70, 21, 21, 21, 1, 1, 1, 6, 8, 14, 14, 3, 3, 3, 1, 1, 5, 5, 21, 21, 21, 39, 39, 21, 1, 8, 8, 14, 14, 14, 14, 14, 14, 14] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 20, 21, 22, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 320 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220067 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220067 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220067/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220067 Building REAL300000220068 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220068' /scratch/stefan/7769801/working/building/REAL300000220068 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220068 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220068/0 /scratch/stefan/7769801/working/building/REAL300000220068 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/68 `/scratch/stefan/7769801/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC) `REAL300000220068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220068 none CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 117, 40, 40, 40, 40, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 40, 40, 56, 153, 153, 153, 153, 153, 40, 40, 40, 9, 9, 3, 3, 2, 2, 2, 1, 56, 56, 56] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 422 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: REAL300000220068 none CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 40, 40, 40, 40, 40, 65, 102, 102, 40, 40, 40, 1, 1, 5, 25, 25, 25, 24, 24, 1, 1, 1, 9, 9, 65, 65, 40, 40, 40, 40, 5, 5, 5] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 22, 23, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 439 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220068 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220068 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220068/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220068 Building REAL300000220069 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220069' /scratch/stefan/7769801/working/building/REAL300000220069 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220069 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220069/0 /scratch/stefan/7769801/working/building/REAL300000220069 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/69 `/scratch/stefan/7769801/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC) `REAL300000220069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220069 none CCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 105, 92, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 21, 39, 140, 140, 140, 140, 140, 105, 105, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 21, 39, 39, 39] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 469 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220069 none CCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 11, 9, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 40, 75, 75, 21, 21, 21, 1, 1, 1, 1, 3, 20, 20, 20, 20, 20, 11, 11, 1, 5, 5, 21, 21, 21, 40, 40, 21, 1, 1, 3, 3, 3] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 42, 43, 21, 22, 23, 24] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 354 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220069 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220069 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220069/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220069 Building REAL300000220070 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220070' /scratch/stefan/7769801/working/building/REAL300000220070 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220070 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220070/0 /scratch/stefan/7769801/working/building/REAL300000220070 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/70 `/scratch/stefan/7769801/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)S2)=N1) `REAL300000220070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220070 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [27, 27, 27, 27, 32, 32, 32, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 32, 32, 27, 9, 9, 1, 1] 32 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 74 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: REAL300000220070 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 1, 9, 9, 27, 27] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 69 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220070 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220070 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220070/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220070 Building REAL300000220071 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220071' /scratch/stefan/7769801/working/building/REAL300000220071 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220071 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220071/0 /scratch/stefan/7769801/working/building/REAL300000220071 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/71 `/scratch/stefan/7769801/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N=C3C=CC=CN32)N1) `REAL300000220071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220071 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N=C3C=CC=CN32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [35, 35, 35, 35, 51, 51, 51, 31, 35, 35, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 51, 51, 9, 9, 1, 1, 1, 1, 35] 51 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 161 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: REAL300000220071 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N=C3C=CC=CN32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 10, 10, 35, 35, 29, 35, 1] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220071 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220071 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220071/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220071 Building REAL300000220072 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220072' /scratch/stefan/7769801/working/building/REAL300000220072 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220072 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220072/0 /scratch/stefan/7769801/working/building/REAL300000220072 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/72 `/scratch/stefan/7769801/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1OC) `REAL300000220072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220072 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 130, 32, 32, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 32, 32, 32, 32, 32, 68, 160, 160, 160, 160, 160, 32, 9, 9, 2, 2, 2, 3, 3, 1, 32, 68, 68, 68] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 448 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220072 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 9, 1, 1, 1, 1, 1, 5, 5, 32, 32, 32, 32, 32, 58, 92, 92, 32, 32, 32, 1, 1, 1, 1, 1, 4, 27, 27, 27, 27, 27, 1, 5, 5, 32, 32, 32, 58, 58, 32, 1, 4, 4, 4] 201 rigid atoms, others: [2, 3, 4, 5, 6, 40, 20, 21, 22, 23, 24, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 417 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220072 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220072 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220072/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220072 Building REAL300000220073 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220073' /scratch/stefan/7769801/working/building/REAL300000220073 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220073 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220073/0 /scratch/stefan/7769801/working/building/REAL300000220073 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/73 `/scratch/stefan/7769801/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC) `REAL300000220073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220073 none C#CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 61, 26, 26, 26, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 26, 26, 26, 47, 85, 146, 146, 146, 26, 26, 9, 9, 2, 2, 2, 3, 3, 1, 26, 85, 85, 85, 85, 85] 201 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 679 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220073 none C#CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 5, 1, 1, 1, 1, 1, 1, 5, 5, 26, 26, 26, 26, 26, 43, 66, 66, 26, 26, 26, 1, 1, 1, 3, 11, 19, 19, 19, 1, 1, 5, 5, 26, 26, 26, 43, 43, 26, 1, 11, 11, 12, 12, 12] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 40, 22, 23, 24, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 314 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220073 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220073 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220073/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220073 Building REAL300000220074 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220074' /scratch/stefan/7769801/working/building/REAL300000220074 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220074 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220074/0 /scratch/stefan/7769801/working/building/REAL300000220074 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/74 `/scratch/stefan/7769801/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220074 none C=CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 106, 96, 30, 30, 30, 30, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 30, 154, 154, 154, 106, 106, 30, 30, 30, 10, 10, 3, 3, 2, 2, 2, 1, 30] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 406 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220074 none C=CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 12, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 30, 30, 30, 30, 30, 56, 91, 91, 30, 30, 30, 1, 36, 36, 36, 12, 12, 1, 1, 1, 5, 5, 56, 56, 30, 30, 30, 30, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 40, 23, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 432 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220074 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220074 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220074/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220074 Building REAL300000220075 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220075' /scratch/stefan/7769801/working/building/REAL300000220075 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220075 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220075/0 /scratch/stefan/7769801/working/building/REAL300000220075 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/75 `/scratch/stefan/7769801/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC(C)C) `REAL300000220075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220075 none COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 51, 51, 51, 51, 51, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 51, 51, 120, 161, 161, 93, 93, 93, 51, 51, 51, 10, 10, 3, 3, 2, 2, 2, 1, 161, 161, 161, 161, 161, 161, 161] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 501 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: REAL300000220075 none COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 51, 51, 51, 51, 51, 86, 142, 142, 51, 51, 51, 1, 1, 4, 10, 10, 4, 4, 4, 1, 1, 1, 9, 9, 86, 86, 51, 51, 51, 51, 10, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 558 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220075 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220075 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220075/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220075 Building REAL300000220076 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220076' /scratch/stefan/7769801/working/building/REAL300000220076 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220076 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220076/0 /scratch/stefan/7769801/working/building/REAL300000220076 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/76 `/scratch/stefan/7769801/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=C(Cl)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220076 none CCOC1=C(Cl)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 85, 48, 48, 48, 48, 48, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 48, 48, 48, 110, 163, 163, 163, 163, 163, 48, 12, 12, 2, 2, 2, 3, 3, 1, 48, 110, 110, 110] 201 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 679 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220076 none CCOC1=C(Cl)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 48, 48, 48, 48, 48, 85, 117, 117, 48, 48, 48, 1, 1, 1, 3, 12, 12, 12, 12, 12, 1, 5, 5, 48, 48, 48, 85, 85, 48, 1, 4, 4, 4] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 40, 22, 23, 24, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 455 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220076 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220076 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220076/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220076 Building REAL300000220077 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220077' /scratch/stefan/7769801/working/building/REAL300000220077 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220077 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220077/0 /scratch/stefan/7769801/working/building/REAL300000220077 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/77 `/scratch/stefan/7769801/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=CC=C1OCC) `REAL300000220077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220077 none CCCOC1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=CC=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 56, 40, 32, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 32, 32, 32, 32, 32, 87, 114, 99, 99, 99, 99, 99, 56, 56, 9, 9, 2, 2, 2, 3, 3, 1, 32, 32, 32, 114, 114, 114, 114, 114] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 613 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220077 none CCCOC1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=CC=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 3, 1, 1, 1, 1, 9, 9, 32, 32, 32, 32, 32, 42, 72, 72, 32, 32, 32, 1, 1, 1, 1, 1, 7, 23, 13, 13, 13, 13, 13, 7, 7, 9, 9, 32, 32, 32, 42, 42, 32, 1, 1, 1, 23, 23, 23, 23, 23] 201 rigid atoms, others: [3, 4, 5, 6, 42, 43, 44, 20, 21, 22, 23, 24] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 49]) total number of confs: 348 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220077 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220077 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220077/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220077 Building REAL300000220078 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220078' /scratch/stefan/7769801/working/building/REAL300000220078 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220078 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220078/0 /scratch/stefan/7769801/working/building/REAL300000220078 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/78 `/scratch/stefan/7769801/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC) `REAL300000220078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220078 none CCCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 90, 83, 20, 20, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 20, 20, 20, 20, 37, 147, 147, 147, 147, 147, 147, 147, 90, 90, 20, 5, 5, 2, 2, 2, 3, 3, 1, 20, 20, 37, 37, 37] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 505 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220078 none CCCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 9, 7, 1, 1, 1, 1, 1, 5, 5, 20, 20, 20, 20, 20, 36, 57, 57, 20, 20, 20, 1, 1, 1, 1, 3, 20, 20, 20, 20, 20, 20, 20, 9, 9, 1, 5, 5, 20, 20, 20, 36, 36, 20, 1, 1, 3, 3, 3] 201 rigid atoms, others: [36, 5, 6, 7, 8, 45, 46, 25, 22, 23, 24, 4] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 286 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220078 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220078 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220078/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220078 Building REAL300000220079 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220079' /scratch/stefan/7769801/working/building/REAL300000220079 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220079 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220079/0 /scratch/stefan/7769801/working/building/REAL300000220079 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/79 `/scratch/stefan/7769801/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220079 none CCCCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 130, 130, 52, 52, 11, 11, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 52, 52, 21, 21, 6, 6, 2, 2, 2, 3, 3, 1, 21, 21] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 55, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 56, 57]) total number of confs: 500 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220079 none CCCCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 37, 47, 47, 21, 21, 21, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 1, 5, 5, 21, 21, 21, 37, 37, 21, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 46, 47, 56, 57, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 198 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220079 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220079 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220079/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220079 Building REAL300000220080 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220080' /scratch/stefan/7769801/working/building/REAL300000220080 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220080 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220080/0 /scratch/stefan/7769801/working/building/REAL300000220080 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/80 `/scratch/stefan/7769801/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220080 none CC(=O)NC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 41, 41, 17, 10, 24, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 24, 24, 41, 41, 41, 41, 24, 24, 10, 10, 3, 3, 2, 2, 2, 1, 24, 24] 53 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 179 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: REAL300000220080 none CC(=O)NC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 34, 40, 40, 24, 24, 24, 1, 1, 3, 3, 3, 3, 1, 1, 6, 6, 34, 34, 24, 24, 24, 24, 1, 1] 53 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 22, 23, 38, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220080 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220080 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220080/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220080 Building REAL300000220081 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220081' /scratch/stefan/7769801/working/building/REAL300000220081 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220081 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220081/0 /scratch/stefan/7769801/working/building/REAL300000220081 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/81 `/scratch/stefan/7769801/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2Cl)N1) `REAL300000220081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220081 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [29, 29, 29, 29, 35, 35, 35, 29, 29, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 35, 35, 9, 9, 1, 1, 1, 1, 29] 35 rigid atoms, others: [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, 32, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 81 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220081 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 29, 29, 21, 29, 29, 29, 1, 2, 2, 2, 3, 3, 11, 11, 29, 29, 25, 29, 1] 35 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 20] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 102 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220081 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220081 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220081/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220081 Building REAL300000220082 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220082' /scratch/stefan/7769801/working/building/REAL300000220082 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220082 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220082/0 /scratch/stefan/7769801/working/building/REAL300000220082 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/82 `/scratch/stefan/7769801/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC([N+](=O)[O-])=C2)N1) `REAL300000220082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220082 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC([N+](=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 33, 33, 33, 25, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 25, 25, 25, 33, 33, 6, 6, 1, 1, 1, 1, 25] 33 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 89 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220082 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC([N+](=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 25, 25, 23, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 9, 9, 25, 25, 23, 25, 1] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220082 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220082 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220082/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220082 Building REAL300000220083 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220083' /scratch/stefan/7769801/working/building/REAL300000220083 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220083 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220083/0 /scratch/stefan/7769801/working/building/REAL300000220083 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/83 `/scratch/stefan/7769801/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([N+](=O)[O-])C=C2)N1) `REAL300000220083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220083 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([N+](=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 13] 13 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 19 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: REAL300000220083 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([N+](=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 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: [1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 10, 10, 13, 13, 10, 10, 13, 13, 13, 13, 1, 2, 2, 2, 3, 3, 10, 10, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 63 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220083 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220083 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220083/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220083 Building REAL300000220084 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220084' /scratch/stefan/7769801/working/building/REAL300000220084 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220084 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220084/0 /scratch/stefan/7769801/working/building/REAL300000220084 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/84 `/scratch/stefan/7769801/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=CC=CC=C23)N1) `REAL300000220084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220084 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [29, 29, 29, 29, 41, 41, 41, 29, 29, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 41, 41, 7, 7, 1, 1, 1, 1, 1, 1, 1, 29] 41 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 113 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: REAL300000220084 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 2, 2, 2, 3, 3, 9, 9, 29, 29, 29, 29, 29, 29, 29, 1] 41 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 71 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220084 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220084 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220084/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220084 Building REAL300000220085 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220085' /scratch/stefan/7769801/working/building/REAL300000220085 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220085 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220085/0 /scratch/stefan/7769801/working/building/REAL300000220085 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/85 `/scratch/stefan/7769801/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N(C)C)C=C2)N1) `REAL300000220085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220085 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 15, 15, 21, 21, 21, 15, 15, 15, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 15, 15, 15, 15, 21, 21, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 15] 25 rigid atoms, others: [38, 39, 12, 13, 14, 15, 16, 17, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 67 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: REAL300000220085 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 15, 15, 9, 13, 25, 25, 15, 15, 1, 2, 2, 2, 3, 3, 9, 9, 15, 15, 25, 25, 25, 25, 25, 25, 15, 15, 1] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 40, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220085 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220085 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220085/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220085 Building REAL300000220086 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220086' /scratch/stefan/7769801/working/building/REAL300000220086 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220086 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220086/0 /scratch/stefan/7769801/working/building/REAL300000220086 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/86 `/scratch/stefan/7769801/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220086 none CCN(CC)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [93, 52, 12, 52, 96, 12, 22, 22, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 22, 22, 93, 93, 93, 93, 93, 96, 96, 96, 96, 96, 22, 22, 12, 12, 3, 3, 2, 2, 2, 1, 22, 22] 185 rigid atoms, others: [44, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 609 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: REAL300000220086 none CCN(CC)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 6, 1, 6, 24, 1, 1, 1, 1, 1, 5, 5, 24, 24, 24, 24, 24, 38, 58, 58, 24, 24, 24, 1, 1, 20, 20, 20, 20, 20, 24, 24, 24, 24, 24, 1, 1, 5, 5, 38, 38, 24, 24, 24, 24, 1, 1] 174 rigid atoms, others: [2, 35, 36, 5, 6, 7, 8, 9, 45, 46, 23, 24] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 336 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220086 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220086 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220086/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220086 Building REAL300000220087 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220087' /scratch/stefan/7769801/working/building/REAL300000220087 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220087 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220087/0 /scratch/stefan/7769801/working/building/REAL300000220087 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/87 `/scratch/stefan/7769801/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2)=N1) `REAL300000220087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220087 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [8, 8, 8, 8, 14, 14, 14, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 8, 4, 4, 1, 1, 1, 1] 14 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 52 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: REAL300000220087 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 3, 3, 1, 8, 8, 8, 8, 8, 8] 14 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 40 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220087 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220087 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220087/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220087 Building REAL300000220088 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220088' /scratch/stefan/7769801/working/building/REAL300000220088 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220088 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220088/0 /scratch/stefan/7769801/working/building/REAL300000220088 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/88 `/scratch/stefan/7769801/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)C=C2)N1) `REAL300000220088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220088 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 13] 13 rigid atoms, others: [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, 32, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 19 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: REAL300000220088 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 9, 9, 13, 13, 9, 11, 13, 13, 1, 2, 2, 2, 3, 3, 9, 9, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 20] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 55 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220088 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220088 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220088/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220088 Building REAL300000220089 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220089' /scratch/stefan/7769801/working/building/REAL300000220089 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220089 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220089/0 /scratch/stefan/7769801/working/building/REAL300000220089 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/89 `/scratch/stefan/7769801/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(OC)=C1OC) `REAL300000220089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220089 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(OC)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [63, 28, 28, 28, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 28, 28, 28, 66, 12, 12, 93, 63, 63, 63, 28, 12, 12, 2, 2, 2, 3, 3, 1, 28, 66, 66, 66, 93, 93, 93] 139 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 322 number of broken/clashed sets: 139 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220089 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(OC)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 4, 4, 28, 28, 28, 28, 28, 48, 76, 76, 28, 28, 28, 1, 1, 1, 3, 1, 1, 6, 4, 4, 4, 1, 4, 4, 28, 28, 28, 48, 48, 28, 1, 3, 3, 3, 7, 7, 7] 139 rigid atoms, others: [1, 2, 3, 4, 5, 38, 19, 20, 21, 23, 24, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 291 number of broken/clashed sets: 139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220089 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220089 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220089/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220089 Building REAL300000220090 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220090' /scratch/stefan/7769801/working/building/REAL300000220090 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220090 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220090/0 /scratch/stefan/7769801/working/building/REAL300000220090 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/90 `/scratch/stefan/7769801/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(F)C=CC=C2Cl)N1) `REAL300000220090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220090 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(F)C=CC=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [31, 31, 31, 31, 41, 41, 41, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 41, 41, 9, 9, 1, 1, 1, 31] 41 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 107 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220090 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(F)C=CC=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 31, 31, 31, 21, 31, 31, 31, 1, 2, 2, 2, 3, 3, 10, 10, 31, 21, 31, 1] 41 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 101 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220090 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220090 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220090/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220090 Building REAL300000220091 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220091' /scratch/stefan/7769801/working/building/REAL300000220091 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220091 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220091/0 /scratch/stefan/7769801/working/building/REAL300000220091 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/91 `/scratch/stefan/7769801/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCCOC3=C2)N1) `REAL300000220091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220091 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCCOC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 4, 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: [18, 18, 18, 18, 27, 27, 27, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 27, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 18] 27 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 83 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: REAL300000220091 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCCOC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 3, 8, 8, 18, 18, 18, 18, 18, 18, 18, 1] 27 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220091 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220091 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220091/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220091 Building REAL300000220092 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220092' /scratch/stefan/7769801/working/building/REAL300000220092 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220092 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220092/0 /scratch/stefan/7769801/working/building/REAL300000220092 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/92 `/scratch/stefan/7769801/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC(F)F)N1) `REAL300000220092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220092 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC(F)F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 97, 132, 132, 58, 58, 58, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 42, 42, 58, 58, 58, 58, 97, 97, 9, 9, 1, 1, 1, 1, 42, 58] 193 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 580 number of broken/clashed sets: 193 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220092 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC(F)F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 58, 58, 20, 58, 58, 58, 125, 172, 172, 1, 2, 2, 2, 3, 3, 12, 12, 58, 58, 58, 58, 172, 1] 193 rigid atoms, others: [0, 1, 2, 3, 36, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 587 number of broken/clashed sets: 193 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220092 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220092 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220092/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220092 Building REAL300000220093 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220093' /scratch/stefan/7769801/working/building/REAL300000220093 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220093 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220093/0 /scratch/stefan/7769801/working/building/REAL300000220093 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/93 `/scratch/stefan/7769801/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Br)=C2)=N1) `REAL300000220093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220093 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [18, 18, 18, 18, 32, 32, 32, 18, 18, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 32, 32, 18, 7, 7, 1, 1, 1, 1] 32 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 116 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: REAL300000220093 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 7, 7, 1, 1, 1, 1, 1, 7, 7, 18, 18, 13, 18, 18, 18, 1, 2, 2, 2, 3, 3, 1, 7, 7, 18, 18, 18, 18] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 84 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220093 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220093 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220093/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220093 Building REAL300000220094 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220094' /scratch/stefan/7769801/working/building/REAL300000220094 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220094 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220094/0 /scratch/stefan/7769801/working/building/REAL300000220094 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/94 `/scratch/stefan/7769801/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2[N+](=O)[O-])N1) `REAL300000220094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220094 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2[N+](=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 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, 26, 26, 26, 35, 35, 35, 26, 26, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 26, 26, 26, 26, 35, 35, 7, 7, 1, 1, 1, 1, 26] 35 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 96 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: REAL300000220094 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2[N+](=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 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, 3, 6, 6, 1, 1, 1, 1, 1, 10, 10, 26, 26, 18, 26, 26, 26, 26, 26, 1, 2, 2, 2, 3, 3, 10, 10, 26, 26, 18, 26, 1] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 90 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220094 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220094 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220094/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220094 Building REAL300000220095 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220095' /scratch/stefan/7769801/working/building/REAL300000220095 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220095 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220095/0 /scratch/stefan/7769801/working/building/REAL300000220095 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/95 `/scratch/stefan/7769801/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC) `REAL300000220095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220095 none COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [131, 70, 70, 70, 70, 70, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 70, 70, 136, 131, 131, 131, 70, 70, 70, 12, 12, 3, 3, 2, 2, 2, 1, 136, 136, 136] 179 rigid atoms, others: [37, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 331 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: REAL300000220095 none COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 70, 70, 70, 70, 70, 107, 156, 156, 70, 70, 70, 1, 1, 7, 4, 4, 4, 1, 1, 1, 9, 9, 107, 107, 70, 70, 70, 70, 7, 7, 7] 179 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 512 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220095 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220095 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220095/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220095 Building REAL300000220096 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220096' /scratch/stefan/7769801/working/building/REAL300000220096 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220096 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220096/0 /scratch/stefan/7769801/working/building/REAL300000220096 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/96 `/scratch/stefan/7769801/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C=C2Cl)=N1) `REAL300000220096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220096 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [15, 15, 15, 15, 27, 27, 27, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 27, 27, 15, 7, 7, 1, 1, 1] 27 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 99 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: REAL300000220096 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 3, 1, 9, 9, 15, 15, 15] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 54 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220096 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220096 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220096/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220096 Building REAL300000220097 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220097' /scratch/stefan/7769801/working/building/REAL300000220097 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220097 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220097/0 /scratch/stefan/7769801/working/building/REAL300000220097 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/97 `/scratch/stefan/7769801/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C=C2)=N1) `REAL300000220097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220097 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 31, 50, 50, 19, 19, 19, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 19, 19, 19, 19, 31, 31, 19, 4, 4, 1, 1, 10, 10, 10, 11, 10, 11, 10, 10, 1, 1] 63 rigid atoms, others: [34, 35, 44, 45, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 189 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220097 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 63, 63, 63, 52, 52, 52, 19, 19, 2, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 52, 52, 52, 52, 63, 63, 52, 19, 19, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 63 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45]) total number of confs: 173 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220097 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 19, 19, 11, 11, 52, 52, 52, 52, 52, 19, 19, 1, 2, 2, 2, 3, 3, 1, 11, 11, 19, 19, 52, 52, 52, 52, 52, 52, 52, 52, 19, 19] 63 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 131 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220097 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220097 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220097/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220097 Building REAL300000220098 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220098' /scratch/stefan/7769801/working/building/REAL300000220098 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220098 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220098/0 /scratch/stefan/7769801/working/building/REAL300000220098 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/98 `/scratch/stefan/7769801/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1OC) `REAL300000220098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220098 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [70, 35, 35, 35, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 35, 35, 35, 67, 70, 70, 70, 35, 35, 11, 11, 3, 3, 2, 2, 2, 1, 35, 67, 67, 67] 109 rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 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: 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: REAL300000220098 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 56, 85, 85, 35, 35, 35, 1, 1, 1, 3, 4, 4, 4, 1, 1, 7, 7, 56, 56, 35, 35, 35, 35, 1, 4, 4, 4] 109 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 27, 28, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 309 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220098 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220098 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220098/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220098 Building REAL300000220099 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220099' /scratch/stefan/7769801/working/building/REAL300000220099 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220099 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220099/0 /scratch/stefan/7769801/working/building/REAL300000220099 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/99 `/scratch/stefan/7769801/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220099 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 17, 21, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 10, 10, 3, 3, 2, 2, 2, 1, 21, 21] 25 rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 76 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: REAL300000220099 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 25, 25, 25, 21, 21, 21, 1, 1, 2, 2, 2, 1, 1, 6, 6, 25, 25, 21, 21, 21, 21, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 20, 21, 25, 26, 36] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 63 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220099 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220099 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220099/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220099 Building REAL300000220100 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220100' /scratch/stefan/7769801/working/building/REAL300000220100 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220100 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220100/0 /scratch/stefan/7769801/working/building/REAL300000220100 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/100 `/scratch/stefan/7769801/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1) `REAL300000220100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220100 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [108, 68, 35, 68, 68, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 68, 68, 89, 68, 108, 108, 108, 68, 68, 11, 11, 3, 3, 2, 2, 2, 1, 89, 89, 89, 68] 157 rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40]) total number of confs: 358 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: REAL300000220100 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 12, 12, 68, 68, 68, 68, 68, 103, 137, 137, 68, 68, 68, 1, 1, 3, 1, 3, 3, 3, 1, 1, 12, 12, 103, 103, 68, 68, 68, 68, 3, 3, 3, 1] 157 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 20, 21, 23, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 448 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220100 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220100 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220100/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220100 Building REAL300000220101 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220101' /scratch/stefan/7769801/working/building/REAL300000220101 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220101 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220101/0 /scratch/stefan/7769801/working/building/REAL300000220101 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/101 `/scratch/stefan/7769801/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(OC(F)F)C=CC3=CC=CC=C32)N1) `REAL300000220101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220101 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(OC(F)F)C=CC3=CC=CC=C32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 73, 117, 117, 41, 41, 41, 7, 7, 1, 1, 1, 1, 7, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 73, 73, 7, 7, 41, 1, 1, 1, 1, 1, 1, 41] 145 rigid atoms, others: [36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42]) total number of confs: 538 number of broken/clashed sets: 144 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220101 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(OC(F)F)C=CC3=CC=CC=C32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 41, 41, 82, 127, 127, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 3, 3, 11, 11, 127, 41, 41, 41, 41, 41, 41, 1] 145 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 27, 42] set([4, 5, 6, 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, 41]) total number of confs: 393 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220101 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220101 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220101/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220101 Building REAL300000220102 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220102' /scratch/stefan/7769801/working/building/REAL300000220102 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220102 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220102/0 /scratch/stefan/7769801/working/building/REAL300000220102 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/102 `/scratch/stefan/7769801/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1OC) `REAL300000220102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220102 none CCOC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 116, 32, 32, 32, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 32, 32, 32, 32, 67, 138, 138, 138, 138, 138, 32, 10, 10, 3, 3, 2, 2, 2, 1, 32, 32, 67, 67, 67] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 375 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: REAL300000220102 none CCOC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 1, 1, 1, 1, 1, 5, 5, 32, 32, 32, 32, 32, 59, 92, 92, 32, 32, 32, 1, 1, 1, 1, 3, 23, 23, 23, 23, 23, 1, 5, 5, 59, 59, 32, 32, 32, 32, 1, 1, 4, 4, 4] 201 rigid atoms, others: [2, 3, 4, 5, 6, 39, 40, 20, 21, 22, 23, 30] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 414 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220102 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220102 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220102/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220102 Building REAL300000220103 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220103' /scratch/stefan/7769801/working/building/REAL300000220103 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220103 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220103/0 /scratch/stefan/7769801/working/building/REAL300000220103 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/103 `/scratch/stefan/7769801/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC2=CC=CC=C2)N1) `REAL300000220103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220103 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 62, 78, 78, 37, 37, 37, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 41, 41, 31, 41, 41, 37, 37, 37, 37, 62, 62, 9, 9, 1, 1, 1, 1, 22, 22, 41, 41, 41, 41, 41, 37] 201 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 406 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220103 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 154, 154, 154, 201, 201, 201, 154, 154, 154, 112, 112, 41, 41, 41, 41, 41, 41, 15, 3, 1, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 201, 201, 112, 112, 41, 41, 41, 41, 3, 3, 1, 1, 1, 1, 1, 154] 201 rigid atoms, others: [41, 42, 43, 44, 45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 620 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220103 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 6, 6, 37, 37, 13, 37, 37, 37, 74, 141, 154, 154, 152, 154, 154, 1, 2, 2, 2, 3, 3, 6, 6, 37, 37, 37, 37, 141, 141, 154, 154, 154, 154, 154, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 46, 27] set([4, 5, 6, 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, 41, 42, 43, 44, 45]) total number of confs: 573 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220103 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220103 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220103/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220103 Building REAL300000220104 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220104' /scratch/stefan/7769801/working/building/REAL300000220104 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220104 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220104/0 /scratch/stefan/7769801/working/building/REAL300000220104 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/104 `/scratch/stefan/7769801/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220104 none CCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 64, 57, 16, 16, 25, 25, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 25, 25, 127, 127, 127, 127, 127, 127, 127, 127, 127, 64, 64, 25, 25, 10, 10, 2, 2, 2, 3, 3, 1, 25, 25] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 495 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220104 none CCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 5, 5, 25, 25, 25, 25, 25, 45, 67, 67, 25, 25, 25, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 1, 1, 5, 5, 25, 25, 25, 45, 45, 25, 1, 1] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 47, 48, 24, 25, 38, 5] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 301 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220104 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220104 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220104/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220104 Building REAL300000220105 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220105' /scratch/stefan/7769801/working/building/REAL300000220105 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220105 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220105/0 /scratch/stefan/7769801/working/building/REAL300000220105 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/105 `/scratch/stefan/7769801/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C2NC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C2=CC=C1) `REAL300000220105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220105 none CCC1=C2NC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [88, 58, 58, 58, 58, 58, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 58, 58, 58, 58, 88, 88, 88, 88, 88, 58, 58, 12, 12, 3, 3, 2, 2, 2, 1, 58, 58, 58] 121 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 286 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: REAL300000220105 none CCC1=C2NC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 58, 58, 58, 58, 58, 88, 94, 94, 58, 58, 58, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 11, 12, 88, 88, 58, 58, 58, 58, 1, 1, 1] 121 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 40, 41, 42, 21, 22, 23, 24, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 305 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220105 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220105 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220105/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220105 Building REAL300000220106 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220106' /scratch/stefan/7769801/working/building/REAL300000220106 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220106 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220106/0 /scratch/stefan/7769801/working/building/REAL300000220106 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/106 `/scratch/stefan/7769801/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)O2)=N1) `REAL300000220106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220106 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [42, 41, 42, 42, 62, 94, 94, 42, 42, 42, 9, 9, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 12, 12, 12, 1, 41, 42, 42, 42, 62, 62, 42, 9, 9, 1, 1, 12, 12, 1, 12] 201 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 334 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220106 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [151, 151, 151, 151, 201, 201, 201, 151, 151, 151, 41, 41, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 151, 151, 151, 151, 201, 201, 151, 41, 41, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 526 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220106 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 42, 42, 42, 42, 151, 151, 42, 151, 151, 151, 151, 151, 42, 1, 2, 2, 2, 3, 3, 1, 11, 11, 42, 42, 151, 151, 52, 151] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 407 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220106 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220106 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220106/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220106 Building REAL300000220107 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220107' /scratch/stefan/7769801/working/building/REAL300000220107 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220107 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220107/0 /scratch/stefan/7769801/working/building/REAL300000220107 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/107 `/scratch/stefan/7769801/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)O2)=N1) `REAL300000220107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220107 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 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: [66, 65, 66, 66, 92, 98, 98, 66, 66, 66, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 1, 2, 7, 7, 7, 7, 1, 65, 66, 66, 66, 92, 92, 66, 13, 13, 1, 1, 7, 7, 7, 7] 143 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 302 number of broken/clashed sets: 142 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220107 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 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: [120, 120, 120, 120, 143, 143, 143, 120, 120, 120, 51, 51, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 120, 120, 120, 120, 143, 143, 120, 51, 51, 7, 7, 1, 1, 1, 1] 143 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 346 number of broken/clashed sets: 142 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220107 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 66, 66, 66, 66, 120, 120, 66, 73, 120, 120, 120, 120, 66, 1, 2, 2, 2, 3, 3, 1, 12, 12, 66, 66, 120, 120, 120, 120] 143 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 495 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220107 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220107 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220107/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220107 Building REAL300000220108 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220108' /scratch/stefan/7769801/working/building/REAL300000220108 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220108 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220108/0 /scratch/stefan/7769801/working/building/REAL300000220108 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/108 `/scratch/stefan/7769801/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1) `REAL300000220108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220108 none COC(=O)C1=CC=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 9, 35, 9, 9, 7, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 29, 41, 41, 17, 17, 17, 1, 35, 35, 35, 9, 9, 9, 9, 1, 1, 3, 3, 18, 18, 18, 29, 29, 17] 201 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 231 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220108 none COC(=O)C1=CC=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 78, 142, 78, 78, 76, 78, 78, 17, 17, 17, 17, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 17, 142, 142, 142, 78, 78, 78, 78, 17, 17, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 360 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220108 none COC(=O)C1=CC=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 18, 18, 78, 78, 78, 78, 78, 131, 152, 152, 78, 78, 78, 9, 9, 9, 9, 1, 1, 1, 1, 9, 9, 18, 18, 78, 78, 78, 131, 131, 78] 201 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 34] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 532 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220108 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220108 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220108/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220108 Building REAL300000220109 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220109' /scratch/stefan/7769801/working/building/REAL300000220109 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220109 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220109/0 /scratch/stefan/7769801/working/building/REAL300000220109 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/109 `/scratch/stefan/7769801/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Br) `REAL300000220109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220109 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [43, 27, 19, 27, 27, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 27, 27, 27, 43, 43, 43, 27, 27, 11, 11, 2, 2, 2, 3, 3, 1, 27] 63 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 142 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: REAL300000220109 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [3, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 44, 63, 63, 27, 27, 27, 1, 1, 1, 4, 4, 4, 1, 1, 6, 6, 27, 27, 27, 44, 44, 27, 1] 63 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 226 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220109 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220109 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220109/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220109 Building REAL300000220110 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220110' /scratch/stefan/7769801/working/building/REAL300000220110 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220110 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220110/0 /scratch/stefan/7769801/working/building/REAL300000220110 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/110 `/scratch/stefan/7769801/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC(C)C)N1) `REAL300000220110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220110 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 119, 164, 164, 71, 71, 71, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 12, 71, 71, 71, 71, 119, 119, 9, 9, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 71] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 583 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220110 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 71, 71, 27, 71, 71, 71, 137, 170, 170, 1, 2, 2, 2, 3, 3, 12, 12, 71, 71, 71, 71, 170, 170, 170, 170, 170, 170, 170, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 42] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 569 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220110 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220110 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220110/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220110 Building REAL300000220111 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220111' /scratch/stefan/7769801/working/building/REAL300000220111 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220111 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220111/0 /scratch/stefan/7769801/working/building/REAL300000220111 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/111 `/scratch/stefan/7769801/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220111 none CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 60, 56, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 38, 122, 122, 122, 122, 122, 122, 122, 60, 60, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 38, 38, 38] 201 rigid atoms, others: [45, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 460 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220111 none CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 9, 5, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 38, 62, 62, 21, 21, 21, 1, 1, 1, 3, 19, 19, 19, 19, 19, 19, 19, 9, 9, 1, 1, 5, 5, 21, 21, 21, 38, 38, 21, 1, 3, 3, 3] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 46, 25, 23, 24, 4, 37] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 306 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220111 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220111 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220111/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220111 Building REAL300000220112 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220112' /scratch/stefan/7769801/working/building/REAL300000220112 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220112 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220112/0 /scratch/stefan/7769801/working/building/REAL300000220112 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/112 `/scratch/stefan/7769801/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220112 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 87, 80, 30, 30, 30, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 30, 30, 30, 64, 135, 135, 135, 135, 135, 87, 87, 30, 30, 9, 9, 2, 2, 2, 3, 3, 1, 30, 64, 64, 64] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 484 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220112 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 12, 7, 1, 1, 1, 1, 1, 1, 5, 5, 30, 30, 30, 30, 30, 55, 88, 88, 30, 30, 30, 1, 1, 1, 3, 20, 20, 20, 20, 20, 12, 12, 1, 1, 5, 5, 30, 30, 30, 55, 55, 30, 1, 4, 4, 4] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 43, 22, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 407 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220112 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220112 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220112/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220112 Building REAL300000220113 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220113' /scratch/stefan/7769801/working/building/REAL300000220113 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220113 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220113/0 /scratch/stefan/7769801/working/building/REAL300000220113 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/113 `/scratch/stefan/7769801/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220113 none C=CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [143, 129, 41, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 21, 21, 21, 44, 143, 143, 143, 129, 129, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 44, 44, 44] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 568 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220113 none C=CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 15, 3, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 40, 69, 69, 21, 21, 21, 1, 1, 1, 3, 39, 39, 39, 15, 15, 1, 1, 5, 5, 21, 21, 21, 40, 40, 21, 1, 3, 3, 3] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 22, 23, 24, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 379 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220113 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220113 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220113/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220113 Building REAL300000220114 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220114' /scratch/stefan/7769801/working/building/REAL300000220114 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220114 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220114/0 /scratch/stefan/7769801/working/building/REAL300000220114 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/114 `/scratch/stefan/7769801/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)O2)=N1) `REAL300000220114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220114 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [62, 61, 62, 62, 92, 120, 120, 62, 62, 62, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 2, 2, 7, 7, 1, 61, 62, 62, 62, 92, 92, 62, 13, 13, 1, 1, 7, 7, 7, 7] 121 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 396 number of broken/clashed sets: 120 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220114 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 121, 121, 121, 98, 98, 98, 42, 42, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 98, 98, 98, 98, 121, 121, 98, 42, 42, 7, 7, 1, 1, 1, 1] 121 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 306 number of broken/clashed sets: 120 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220114 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 62, 62, 62, 62, 98, 98, 91, 91, 98, 98, 62, 1, 2, 2, 2, 3, 3, 1, 12, 12, 62, 62, 98, 98, 98, 98] 121 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 197 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220114 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220114 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220114/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220114 Building REAL300000220115 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220115' /scratch/stefan/7769801/working/building/REAL300000220115 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220115 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220115/0 /scratch/stefan/7769801/working/building/REAL300000220115 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/115 `/scratch/stefan/7769801/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)O2)=N1) `REAL300000220115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220115 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 94, 101, 101, 66, 66, 66, 12, 12, 1, 1, 1, 1, 1, 1, 10, 10, 1, 10, 10, 10, 1, 66, 66, 66, 66, 94, 94, 66, 12, 12, 1, 1, 10, 10, 2, 10] 201 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 309 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220115 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 166, 201, 201, 201, 166, 166, 166, 63, 63, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 166, 166, 166, 166, 201, 201, 166, 63, 63, 10, 10, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 471 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220115 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 13, 13, 66, 66, 66, 66, 166, 166, 95, 166, 166, 166, 66, 1, 2, 2, 2, 3, 3, 1, 13, 13, 66, 66, 166, 166, 151, 166] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 518 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220115 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220115 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220115/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220115 Building REAL300000220116 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220116' /scratch/stefan/7769801/working/building/REAL300000220116 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220116 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220116/0 /scratch/stefan/7769801/working/building/REAL300000220116 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/116 `/scratch/stefan/7769801/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=C(C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)OC(C)C2) `REAL300000220116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220116 none COC1=CC2=C(C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)OC(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [71, 56, 56, 56, 56, 56, 56, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 56, 56, 56, 56, 71, 71, 71, 56, 56, 11, 11, 3, 3, 2, 2, 2, 1, 56, 56, 56, 56, 56, 56] 91 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 131 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: REAL300000220116 none COC1=CC2=C(C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)OC(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 56, 56, 56, 56, 56, 83, 91, 91, 56, 56, 56, 1, 1, 1, 1, 4, 4, 4, 1, 1, 11, 11, 83, 83, 56, 56, 56, 56, 1, 2, 2, 2, 1, 1] 91 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 39, 44, 43, 22, 23, 24, 25, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 287 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220116 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220116 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220116/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220116 Building REAL300000220117 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220117' /scratch/stefan/7769801/working/building/REAL300000220117 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220117 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220117/0 /scratch/stefan/7769801/working/building/REAL300000220117 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/117 `/scratch/stefan/7769801/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C=C2)N1) `REAL300000220117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220117 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [13, 13, 13, 13, 24, 25, 25, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 13, 13, 13, 13, 24, 24, 3, 3, 1, 1, 4, 3, 1, 1, 13] 26 rigid atoms, others: [32, 33, 36, 37, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38]) total number of confs: 94 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220117 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [25, 25, 25, 25, 26, 26, 26, 25, 25, 25, 6, 6, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 25, 25, 25, 25, 26, 26, 6, 6, 4, 4, 1, 1, 4, 4, 25] 26 rigid atoms, others: [34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 26 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220117 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 9, 9, 25, 25, 25, 25, 13, 13, 1, 2, 2, 2, 3, 3, 9, 9, 13, 13, 25, 25, 13, 13, 1] 26 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 81 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220117 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220117 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220117/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220117 Building REAL300000220118 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220118' /scratch/stefan/7769801/working/building/REAL300000220118 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220118 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220118/0 /scratch/stefan/7769801/working/building/REAL300000220118 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/118 `/scratch/stefan/7769801/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)S2)N1) `REAL300000220118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220118 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [51, 51, 51, 51, 63, 63, 63, 51, 51, 51, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 51, 51, 51, 51, 63, 63, 13, 13, 1, 1, 7, 7, 2, 7, 7, 51] 94 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 165 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220118 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [82, 82, 82, 82, 94, 94, 94, 82, 82, 82, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 82, 82, 82, 82, 94, 94, 50, 50, 7, 7, 1, 1, 1, 1, 1, 82] 94 rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 230 number of broken/clashed sets: 93 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220118 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 6, 6, 1, 1, 1, 1, 1, 10, 10, 51, 51, 51, 51, 82, 82, 57, 82, 82, 51, 1, 2, 2, 2, 3, 3, 10, 10, 51, 51, 82, 82, 76, 82, 82, 1] 94 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 257 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220118 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220118 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220118/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220118 Building REAL300000220119 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220119' /scratch/stefan/7769801/working/building/REAL300000220119 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220119 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220119/0 /scratch/stefan/7769801/working/building/REAL300000220119 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/119 `/scratch/stefan/7769801/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN(C3=CC=CC=C3)N=C2)N1) `REAL300000220119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220119 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [32, 32, 32, 32, 49, 49, 49, 32, 32, 32, 12, 12, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 32, 33, 33, 33, 49, 49, 12, 12, 4, 4, 2, 4, 4, 1, 31] 49 rigid atoms, others: [37, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 170 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220119 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [35, 35, 35, 35, 49, 49, 49, 35, 35, 35, 20, 20, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 49, 49, 20, 20, 1, 1, 1, 1, 1, 4, 35] 49 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 153 number of broken/clashed sets: 48 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220119 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 32, 32, 32, 35, 35, 35, 35, 35, 32, 32, 1, 2, 2, 2, 3, 3, 10, 10, 35, 35, 35, 35, 35, 32, 1] 49 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 85 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220119 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220119 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220119/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220119 Building REAL300000220120 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220120' /scratch/stefan/7769801/working/building/REAL300000220120 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220120 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220120/0 /scratch/stefan/7769801/working/building/REAL300000220120 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/120 `/scratch/stefan/7769801/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1) `REAL300000220120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220120 none COC1=CC(OC)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [97, 22, 21, 58, 58, 58, 96, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 58, 58, 93, 58, 97, 97, 97, 58, 96, 96, 96, 12, 12, 3, 3, 2, 2, 2, 1, 93, 93, 93, 58] 185 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 415 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: REAL300000220120 none COC1=CC(OC)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 1, 1, 8, 8, 58, 57, 58, 58, 58, 95, 142, 142, 58, 58, 58, 1, 1, 3, 1, 2, 2, 2, 1, 4, 4, 4, 8, 8, 95, 95, 58, 58, 58, 58, 4, 4, 4, 1] 185 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 44, 22, 23, 25, 29] set([0, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 507 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220120 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220120 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220120/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220120 Building REAL300000220121 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220121' /scratch/stefan/7769801/working/building/REAL300000220121 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220121 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220121/0 /scratch/stefan/7769801/working/building/REAL300000220121 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/121 `/scratch/stefan/7769801/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CCC#N)N=C2C2=CC=CC=C2)N1) `REAL300000220121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220121 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CCC#N)N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.1', 'N.1', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 72, 89, 89, 42, 42, 42, 11, 11, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 1, 6, 6, 2, 6, 6, 42, 43, 43, 43, 72, 72, 11, 11, 1, 6, 6, 10, 10, 6, 6, 5, 6, 6, 42] 201 rigid atoms, others: [36, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 367 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220121 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CCC#N)N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.1', 'N.1', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 102, 116, 116, 65, 65, 65, 23, 23, 6, 6, 6, 6, 6, 19, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 102, 102, 23, 23, 6, 19, 19, 27, 27, 1, 1, 1, 1, 1, 65] 201 rigid atoms, others: [41, 42, 43, 44, 45, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 477 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220121 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CCC#N)N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.1', 'N.1', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 42, 42, 42, 111, 140, 140, 42, 42, 42, 65, 65, 57, 65, 65, 1, 2, 2, 2, 3, 3, 9, 9, 42, 111, 111, 140, 140, 65, 65, 64, 65, 65, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 46, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 641 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220121 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220121 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220121/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220121 Building REAL300000220122 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220122' /scratch/stefan/7769801/working/building/REAL300000220122 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220122 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220122/0 /scratch/stefan/7769801/working/building/REAL300000220122 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/122 `/scratch/stefan/7769801/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCOC3=C2)=N1) `REAL300000220122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220122 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 21, 21, 21, 31, 31, 31, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 31, 31, 21, 6, 6, 1, 1, 1, 1] 31 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 94 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: REAL300000220122 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 9, 9, 21, 21, 21, 21] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 65 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220122 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220122 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220122/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220122 Building REAL300000220123 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220123' /scratch/stefan/7769801/working/building/REAL300000220123 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220123 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220123/0 /scratch/stefan/7769801/working/building/REAL300000220123 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/123 `/scratch/stefan/7769801/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C2O1) `REAL300000220123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220123 none CCCCC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 115, 99, 39, 39, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 117, 117, 117, 117, 117, 115, 115, 99, 99, 9, 9, 3, 3, 1, 1, 1, 1, 39, 39, 39, 39] 201 rigid atoms, others: [43, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 41, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47]) 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: REAL300000220123 none CCCCC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 9, 5, 1, 1, 1, 1, 9, 9, 39, 39, 39, 39, 39, 67, 95, 95, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 11, 11, 10, 10, 5, 5, 9, 9, 67, 67, 39, 39, 39, 39, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220123 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220123 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220123/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220123 Building REAL300000220124 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220124' /scratch/stefan/7769801/working/building/REAL300000220124 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220124 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220124/0 /scratch/stefan/7769801/working/building/REAL300000220124 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/124 `/scratch/stefan/7769801/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC(F)F) `REAL300000220124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220124 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 40, 40, 40, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 40, 40, 40, 40, 92, 145, 145, 86, 86, 86, 40, 11, 11, 2, 2, 2, 3, 3, 1, 40, 40, 145] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 551 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220124 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 40, 40, 40, 40, 40, 67, 104, 104, 40, 40, 40, 1, 1, 1, 1, 5, 20, 20, 4, 4, 4, 1, 5, 5, 40, 40, 40, 67, 67, 40, 1, 1, 20] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 19, 20, 21, 22, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 429 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220124 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220124 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220124/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220124 Building REAL300000220125 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220125' /scratch/stefan/7769801/working/building/REAL300000220125 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220125 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220125/0 /scratch/stefan/7769801/working/building/REAL300000220125 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/125 `/scratch/stefan/7769801/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CN=C3C=C2)N1) `REAL300000220125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220125 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CN=C3C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 27, 27, 27, 18, 18, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 27, 27, 5, 5, 1, 1, 1, 1, 1, 1, 18] 27 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 83 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: REAL300000220125 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CN=C3C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 3, 8, 8, 18, 18, 18, 18, 18, 18, 1] 27 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220125 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220125 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220125/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220125 Building REAL300000220126 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220126' /scratch/stefan/7769801/working/building/REAL300000220126 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220126 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220126/0 /scratch/stefan/7769801/working/building/REAL300000220126 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/126 `/scratch/stefan/7769801/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(C)(C)C)C=C2)N1) `REAL300000220126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220126 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(C)(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 13, 25, 25, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 13] 25 rigid atoms, others: [32, 42, 43, 12, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 76 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: REAL300000220126 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(C)(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 11, 11, 25, 25, 25, 13, 13, 1, 2, 2, 2, 3, 3, 9, 9, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 13, 1] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 44, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 128 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220126 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220126 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220126/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220126 Building REAL300000220127 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220127' /scratch/stefan/7769801/working/building/REAL300000220127 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220127 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220127/0 /scratch/stefan/7769801/working/building/REAL300000220127 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/127 `/scratch/stefan/7769801/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C=C2F)N1) `REAL300000220127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220127 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [28, 28, 28, 28, 38, 38, 38, 28, 28, 28, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 38, 38, 10, 10, 1, 1, 1, 28] 38 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 107 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: REAL300000220127 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 28, 28, 14, 28, 28, 28, 28, 1, 2, 2, 2, 3, 3, 11, 11, 28, 28, 28, 1] 38 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 119 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220127 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220127 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220127/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220127 Building REAL300000220128 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220128' /scratch/stefan/7769801/working/building/REAL300000220128 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220128 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220128/0 /scratch/stefan/7769801/working/building/REAL300000220128 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/128 `/scratch/stefan/7769801/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Cl)=C2Cl)=N1) `REAL300000220128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220128 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Cl)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [27, 27, 27, 27, 35, 35, 35, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 35, 35, 27, 7, 7, 1, 1, 1] 35 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 89 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220128 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Cl)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 1, 11, 11, 27, 27, 27] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 71 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220128 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220128 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220128/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220128 Building REAL300000220129 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220129' /scratch/stefan/7769801/working/building/REAL300000220129 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220129 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220129/0 /scratch/stefan/7769801/working/building/REAL300000220129 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/129 `/scratch/stefan/7769801/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(Cl)=C2)=N1) `REAL300000220129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220129 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 20, 20, 20, 32, 32, 32, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 32, 32, 20, 7, 7, 1, 1, 1] 32 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 106 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: REAL300000220129 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 7, 7, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 1, 8, 8, 20, 20, 20] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 63 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220129 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220129 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220129/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220129 Building REAL300000220130 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220130' /scratch/stefan/7769801/working/building/REAL300000220130 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220130 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220130/0 /scratch/stefan/7769801/working/building/REAL300000220130 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/130 `/scratch/stefan/7769801/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C=C2)=N1) `REAL300000220130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220130 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 49, 78, 78, 28, 28, 28, 4, 4, 1, 1, 1, 1, 1, 1, 13, 43, 43, 1, 1, 28, 28, 28, 28, 49, 49, 28, 4, 4, 1, 1, 43, 1, 1] 187 rigid atoms, others: [32, 33, 35, 36, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 408 number of broken/clashed sets: 187 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220130 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 7, 7, 1, 1, 1, 1, 1, 13, 13, 28, 28, 13, 13, 108, 156, 156, 28, 28, 1, 2, 2, 2, 3, 3, 1, 13, 13, 28, 28, 156, 28, 28] 187 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 479 number of broken/clashed sets: 187 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220130 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220130 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220130/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220130 Building REAL300000220131 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220131' /scratch/stefan/7769801/working/building/REAL300000220131 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220131 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220131/0 /scratch/stefan/7769801/working/building/REAL300000220131 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/131 `/scratch/stefan/7769801/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2C(F)(F)F)=N1) `REAL300000220131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220131 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 28, 35, 35, 35, 28, 28, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 28, 28, 28, 28, 35, 35, 28, 5, 5, 1, 1, 1, 1] 35 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 86 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220131 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 28, 28, 20, 28, 28, 28, 28, 28, 28, 1, 2, 2, 2, 3, 3, 1, 11, 11, 28, 28, 20, 28] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220131 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220131 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220131/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220131 Building REAL300000220132 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220132' /scratch/stefan/7769801/working/building/REAL300000220132 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220132 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220132/0 /scratch/stefan/7769801/working/building/REAL300000220132 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/132 `/scratch/stefan/7769801/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220132 none CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 137, 84, 71, 24, 24, 35, 35, 13, 13, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 35, 35, 142, 142, 142, 142, 142, 137, 137, 84, 84, 35, 35, 13, 13, 2, 2, 2, 3, 3, 1, 35, 35] 201 rigid atoms, others: [43, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 551 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220132 none CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 4, 1, 1, 1, 1, 1, 1, 5, 5, 35, 35, 35, 35, 35, 63, 98, 98, 35, 35, 35, 1, 1, 20, 20, 20, 20, 20, 16, 16, 6, 6, 1, 1, 5, 5, 35, 35, 35, 63, 63, 35, 1, 1] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 44, 45, 23, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 430 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220132 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220132 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220132/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220132 Building REAL300000220133 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220133' /scratch/stefan/7769801/working/building/REAL300000220133 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220133 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220133/0 /scratch/stefan/7769801/working/building/REAL300000220133 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/133 `/scratch/stefan/7769801/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCCC(C)C)C=C2)=N1) `REAL300000220133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220133 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCCC(C)C)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 33, 54, 54, 19, 19, 19, 4, 4, 1, 1, 1, 1, 1, 1, 7, 11, 21, 25, 25, 1, 1, 19, 19, 19, 19, 33, 33, 19, 4, 4, 1, 1, 11, 11, 21, 21, 25, 25, 25, 25, 25, 25, 25, 1, 1] 201 rigid atoms, others: [48, 34, 35, 12, 13, 14, 15, 16, 17, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 308 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220133 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCCC(C)C)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 19, 19, 12, 12, 69, 76, 106, 129, 129, 19, 19, 1, 2, 2, 2, 3, 3, 1, 12, 12, 19, 19, 76, 76, 106, 106, 129, 129, 129, 129, 129, 129, 129, 19, 19] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 513 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220133 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220133 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220133/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220133 Building REAL300000220134 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220134' /scratch/stefan/7769801/working/building/REAL300000220134 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220134 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220134/0 /scratch/stefan/7769801/working/building/REAL300000220134 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/134 `/scratch/stefan/7769801/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220134 none CCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 126, 126, 126, 54, 54, 13, 13, 21, 21, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 54, 54, 21, 21, 9, 9, 2, 2, 2, 3, 3, 1, 21, 21] 201 rigid atoms, others: [49, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 481 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220134 none CCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 36, 56, 56, 21, 21, 21, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 1, 5, 5, 21, 21, 21, 36, 36, 21, 1, 1] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 40, 50, 51, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 232 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220134 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220134 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220134/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220134 Building REAL300000220135 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220135' /scratch/stefan/7769801/working/building/REAL300000220135 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220135 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220135/0 /scratch/stefan/7769801/working/building/REAL300000220135 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/135 `/scratch/stefan/7769801/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC3=CC=CC=C3)=C2)N1) `REAL300000220135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220135 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC3=CC=CC=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 39, 44, 44, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 9, 14, 14, 10, 14, 14, 1, 22, 22, 22, 22, 39, 39, 5, 5, 1, 1, 1, 14, 14, 14, 14, 14, 1, 22] 201 rigid atoms, others: [34, 35, 36, 42, 12, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 43]) total number of confs: 188 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220135 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC3=CC=CC=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 201, 201, 201, 120, 120, 120, 42, 42, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 14, 120, 120, 120, 120, 201, 201, 42, 42, 14, 14, 14, 1, 1, 1, 1, 1, 14, 120] 201 rigid atoms, others: [37, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43]) total number of confs: 690 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220135 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC3=CC=CC=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 104, 120, 120, 119, 120, 120, 22, 1, 2, 2, 2, 3, 3, 7, 7, 22, 22, 22, 120, 120, 120, 120, 120, 22, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 43, 26] set([4, 5, 6, 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, 41, 42]) total number of confs: 199 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220135 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220135 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220135/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220135 Building REAL300000220136 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220136' /scratch/stefan/7769801/working/building/REAL300000220136 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220136 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220136/0 /scratch/stefan/7769801/working/building/REAL300000220136 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/136 `/scratch/stefan/7769801/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(OCCC)=C1) `REAL300000220136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220136 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(OCCC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 12, 9, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 12, 12, 20, 27, 52, 12, 61, 61, 61, 61, 61, 35, 35, 12, 12, 7, 7, 2, 2, 2, 3, 3, 1, 27, 27, 53, 53, 53, 53, 53, 12] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 389 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220136 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(OCCC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 17, 27, 27, 12, 12, 12, 1, 1, 5, 12, 23, 1, 14, 14, 14, 14, 14, 6, 6, 1, 1, 6, 6, 12, 12, 12, 17, 17, 12, 12, 12, 24, 24, 24, 24, 24, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 3, 52, 22, 23, 36, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220136 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220136 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220136/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220136 Building REAL300000220137 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220137' /scratch/stefan/7769801/working/building/REAL300000220137 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220137 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220137/0 /scratch/stefan/7769801/working/building/REAL300000220137 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/137 `/scratch/stefan/7769801/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(=O)[O-])C=C2)N1) `REAL300000220137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220137 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 13, 13, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 13] 13 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 25 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: REAL300000220137 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 9, 11, 13, 13, 13, 13, 1, 2, 2, 2, 3, 3, 9, 9, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220137 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220137 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220137/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220137 Building REAL300000220138 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220138' /scratch/stefan/7769801/working/building/REAL300000220138 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220138 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220138/0 /scratch/stefan/7769801/working/building/REAL300000220138 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/138 `/scratch/stefan/7769801/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2I)=N1) `REAL300000220138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220138 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2I)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [27, 27, 27, 27, 35, 35, 35, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 35, 35, 27, 7, 7, 1, 1, 1, 1] 35 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 89 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220138 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2I)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 27, 27, 13, 27, 27, 27, 1, 2, 2, 2, 3, 3, 1, 11, 11, 27, 27, 25, 27] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 124 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220138 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220138 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220138/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220138 Building REAL300000220139 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220139' /scratch/stefan/7769801/working/building/REAL300000220139 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220139 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220139/0 /scratch/stefan/7769801/working/building/REAL300000220139 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/139 `/scratch/stefan/7769801/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220139 none COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [33, 21, 21, 21, 21, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 33, 33, 33, 21, 21, 21, 10, 10, 3, 3, 2, 2, 2, 1, 21] 61 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 84 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: REAL300000220139 none COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 38, 46, 46, 21, 21, 21, 1, 3, 3, 3, 1, 1, 1, 6, 6, 38, 38, 21, 21, 21, 21, 1] 61 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 25, 26, 27, 36] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220139 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220139 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220139/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220139 Building REAL300000220140 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220140' /scratch/stefan/7769801/working/building/REAL300000220140 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220140 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220140/0 /scratch/stefan/7769801/working/building/REAL300000220140 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/140 `/scratch/stefan/7769801/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220140 none CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 128, 35, 35, 35, 35, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 35, 35, 35, 79, 151, 151, 151, 151, 151, 35, 35, 10, 10, 2, 2, 2, 3, 3, 1, 35, 79, 79, 79] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 405 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220140 none CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 9, 1, 1, 1, 1, 1, 1, 5, 5, 35, 35, 35, 35, 35, 62, 107, 107, 35, 35, 35, 1, 1, 1, 3, 26, 26, 26, 26, 26, 1, 1, 5, 5, 35, 35, 35, 62, 62, 35, 1, 4, 4, 4] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 469 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220140 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220140 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220140/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220140 Building REAL300000220141 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220141' /scratch/stefan/7769801/working/building/REAL300000220141 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220141 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220141/0 /scratch/stefan/7769801/working/building/REAL300000220141 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/141 `/scratch/stefan/7769801/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(C)C)C=C2)N1) `REAL300000220141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220141 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 14, 14, 26, 34, 34, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 14, 14, 14, 14, 26, 26, 3, 3, 1, 1, 4, 5, 5, 5, 5, 5, 5, 1, 1, 14] 41 rigid atoms, others: [39, 40, 12, 13, 14, 15, 16, 17, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 148 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: REAL300000220141 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 14, 14, 9, 9, 36, 36, 14, 14, 1, 2, 2, 2, 3, 3, 9, 9, 14, 14, 36, 36, 36, 36, 36, 36, 36, 14, 14, 1] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 41] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220141 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220141 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220141/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220141 Building REAL300000220142 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220142' /scratch/stefan/7769801/working/building/REAL300000220142 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220142 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220142/0 /scratch/stefan/7769801/working/building/REAL300000220142 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/142 `/scratch/stefan/7769801/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC) `REAL300000220142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220142 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 91, 54, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 46, 46, 146, 146, 146, 146, 146, 91, 91, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 46, 46, 46, 46, 46] 201 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 635 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220142 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 38, 68, 68, 21, 21, 21, 1, 1, 1, 5, 5, 26, 26, 26, 26, 26, 13, 13, 1, 1, 5, 5, 21, 21, 21, 38, 38, 21, 1, 5, 5, 5, 5, 5] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 44, 35, 22, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 365 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220142 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220142 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220142/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220142 Building REAL300000220143 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220143' /scratch/stefan/7769801/working/building/REAL300000220143 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220143 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220143/0 /scratch/stefan/7769801/working/building/REAL300000220143 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/143 `/scratch/stefan/7769801/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1[N+](=O)[O-]) `REAL300000220143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220143 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 3, 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: [14, 14, 21, 21, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 3, 3, 2, 2, 2, 1, 21] 31 rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 117 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: REAL300000220143 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 3, 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, 5, 5, 21, 21, 21, 21, 21, 31, 31, 31, 21, 21, 21, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 5, 5, 31, 31, 21, 21, 21, 21, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 27, 28, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 102 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220143 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220143 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220143/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220143 Building REAL300000220144 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220144' /scratch/stefan/7769801/working/building/REAL300000220144 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220144 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220144/0 /scratch/stefan/7769801/working/building/REAL300000220144 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/144 `/scratch/stefan/7769801/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([O-])C([N+](=O)[O-])=C2)N1) `REAL300000220144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220144 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([O-])C([N+](=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 33, 33, 33, 26, 26, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 26, 26, 26, 26, 33, 33, 6, 6, 1, 1, 1, 26] 33 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 84 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220144 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([O-])C([N+](=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 26, 26, 9, 9, 26, 26, 26, 26, 26, 1, 2, 2, 2, 3, 3, 9, 9, 26, 26, 26, 1] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 97 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220144 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220144 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220144/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220144 Building REAL300000220145 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220145' /scratch/stefan/7769801/working/building/REAL300000220145 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220145 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220145/0 /scratch/stefan/7769801/working/building/REAL300000220145 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/145 `/scratch/stefan/7769801/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3C=C2)N1) `REAL300000220145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220145 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [18, 18, 18, 18, 27, 27, 27, 18, 18, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 27, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 18] 27 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 83 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: REAL300000220145 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 3, 8, 8, 18, 18, 18, 18, 18, 18, 18, 1] 27 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220145 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220145 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220145/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220145 Building REAL300000220146 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220146' /scratch/stefan/7769801/working/building/REAL300000220146 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220146 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220146/0 /scratch/stefan/7769801/working/building/REAL300000220146 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/146 `/scratch/stefan/7769801/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=CC=C1) `REAL300000220146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220146 none COC1=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [55, 40, 40, 40, 40, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 40, 40, 40, 40, 40, 55, 55, 55, 11, 11, 3, 3, 2, 2, 2, 1, 40, 40, 40, 40] 81 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) 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: REAL300000220146 none COC1=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 13, 13, 39, 39, 40, 40, 40, 59, 81, 81, 40, 40, 40, 1, 1, 1, 1, 1, 3, 3, 3, 13, 13, 59, 59, 40, 40, 40, 40, 1, 1, 1, 1] 81 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 20, 21, 22, 23, 24, 36, 38, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220146 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220146 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220146/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220146 Building REAL300000220147 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220147' /scratch/stefan/7769801/working/building/REAL300000220147 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220147 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220147/0 /scratch/stefan/7769801/working/building/REAL300000220147 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/147 `/scratch/stefan/7769801/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(C)C)C([N+](=O)[O-])=C2)=N1) `REAL300000220147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220147 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(C)C)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [23, 23, 23, 23, 33, 33, 33, 23, 23, 23, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 23, 23, 23, 23, 33, 33, 23, 6, 6, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1] 33 rigid atoms, others: [34, 35, 43, 12, 13, 14, 15, 16, 17, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 105 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220147 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(C)C)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 23, 23, 11, 15, 23, 23, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 3, 1, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 138 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220147 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220147 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220147/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220147 Building REAL300000220148 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220148' /scratch/stefan/7769801/working/building/REAL300000220148 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220148 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220148/0 /scratch/stefan/7769801/working/building/REAL300000220148 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/148 `/scratch/stefan/7769801/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=CC=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220148 none CC1=NN(CC2=CC=CC=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 39, 39, 140, 140, 140, 140, 140, 201, 201, 201, 140, 140, 140, 10, 10, 10, 3, 3, 1, 1, 1, 1, 1, 10, 10, 10, 39, 39, 140, 140, 140, 201, 201, 140] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 603 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220148 none CC1=NN(CC2=CC=CC=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 128, 140, 140, 132, 140, 140, 47, 47, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 47, 47, 47, 128, 128, 140, 140, 140, 140, 140, 47, 47, 47, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 523 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220148 none CC1=NN(CC2=CC=CC=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 9, 10, 8, 10, 9, 1, 1, 1, 1, 7, 7, 47, 47, 47, 47, 47, 82, 93, 93, 47, 47, 47, 2, 2, 2, 5, 5, 9, 10, 10, 10, 9, 2, 2, 2, 7, 7, 47, 47, 47, 82, 82, 47] 201 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 363 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220148 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220148 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220148/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220148 Building REAL300000220149 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220149' /scratch/stefan/7769801/working/building/REAL300000220149 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220149 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220149/0 /scratch/stefan/7769801/working/building/REAL300000220149 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/149 `/scratch/stefan/7769801/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(C)C) `REAL300000220149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220149 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 57, 24, 24, 24, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 24, 24, 24, 24, 107, 134, 161, 163, 58, 58, 58, 58, 58, 24, 8, 8, 2, 2, 2, 3, 3, 1, 24, 24, 134, 134, 163, 163, 163, 163, 163, 163, 163] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 560 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220149 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 5, 5, 24, 24, 24, 24, 24, 42, 75, 75, 24, 24, 24, 1, 1, 1, 1, 9, 17, 25, 28, 6, 6, 6, 6, 6, 1, 5, 5, 24, 24, 24, 42, 42, 24, 1, 1, 17, 17, 28, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 42, 43, 20, 21, 22, 23] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 413 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220149 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220149 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220149/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220149 Building REAL300000220150 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220150' /scratch/stefan/7769801/working/building/REAL300000220150 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220150 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220150/0 /scratch/stefan/7769801/working/building/REAL300000220150 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/150 `/scratch/stefan/7769801/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CC=C2F)=N1) `REAL300000220150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220150 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [37, 37, 37, 37, 49, 49, 49, 37, 37, 37, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 49, 49, 37, 11, 11, 1, 1, 1] 49 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 130 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: REAL300000220150 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 37, 37, 37, 31, 37, 37, 37, 1, 2, 2, 2, 3, 3, 1, 9, 9, 37, 37, 37] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 103 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220150 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220150 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220150/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220150 Building REAL300000220151 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220151' /scratch/stefan/7769801/working/building/REAL300000220151 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220151 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220151/0 /scratch/stefan/7769801/working/building/REAL300000220151 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/151 `/scratch/stefan/7769801/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C([N+](=O)[O-])C=C1OC) `REAL300000220151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220151 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C([N+](=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 11, 11, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [88, 39, 39, 39, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 84, 88, 88, 88, 39, 11, 11, 2, 2, 2, 3, 3, 1, 39, 84, 84, 84] 135 rigid atoms, others: [38, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 134 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220151 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C([N+](=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 11, 11, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 7, 7, 39, 39, 39, 39, 39, 65, 107, 107, 39, 39, 39, 1, 1, 2, 2, 1, 1, 1, 3, 4, 4, 4, 1, 7, 7, 39, 39, 39, 65, 65, 39, 1, 4, 4, 4] 135 rigid atoms, others: [1, 2, 3, 4, 5, 39, 19, 20, 23, 24, 25, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 394 number of broken/clashed sets: 134 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220151 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220151 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220151/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220151 Building REAL300000220152 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220152' /scratch/stefan/7769801/working/building/REAL300000220152 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220152 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220152/0 /scratch/stefan/7769801/working/building/REAL300000220152 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/152 `/scratch/stefan/7769801/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2F)=N1) `REAL300000220152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220152 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [19, 19, 19, 19, 33, 33, 33, 19, 19, 19, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 33, 33, 19, 9, 9, 1, 1, 1] 33 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 119 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220152 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 19, 19, 15, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 1, 9, 9, 19, 19, 19] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220152 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220152 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220152/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220152 Building REAL300000220153 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220153' /scratch/stefan/7769801/working/building/REAL300000220153 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220153 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220153/0 /scratch/stefan/7769801/working/building/REAL300000220153 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/153 `/scratch/stefan/7769801/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC([N+](=O)[O-])=C1O) `REAL300000220153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220153 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC([N+](=O)[O-])=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [57, 35, 35, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 57, 57, 57, 35, 11, 11, 2, 2, 2, 3, 3, 1, 35, 70] 140 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 190 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220153 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC([N+](=O)[O-])=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 35, 35, 35, 35, 35, 56, 70, 70, 35, 35, 35, 1, 1, 1, 2, 2, 1, 1, 4, 4, 4, 1, 5, 5, 35, 35, 35, 56, 56, 35, 1, 2] 140 rigid atoms, others: [1, 2, 3, 4, 5, 38, 19, 20, 21, 24, 25, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 242 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220153 /scratch/stefan/7769801/working /scratch/stefan/7769801 mkdir: created directory `1' /scratch/stefan/7769801/working/building/REAL300000220153/1 /scratch/stefan/7769801/working/building/REAL300000220153 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 1 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/154 `/scratch/stefan/7769801/working/3D/154' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC([N+](=O)[O-])=C1[O-]) `REAL300000220153.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220153/1/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: REAL300000220153 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC([N+](=O)[O-])=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [53, 29, 29, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 53, 53, 53, 29, 11, 11, 2, 2, 2, 3, 3, 1, 29] 71 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 117 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220153 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC([N+](=O)[O-])=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 47, 71, 71, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 5, 5, 29, 29, 29, 47, 47, 29, 1] 71 rigid atoms, others: [1, 2, 3, 4, 5, 38, 19, 20, 21, 22, 23, 24, 25, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 247 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220153 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220153 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 1: /scratch/stefan/7769801/working/building/REAL300000220153/1.* 0: /scratch/stefan/7769801/working/building/REAL300000220153/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220153 Building REAL300000220154 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220154' /scratch/stefan/7769801/working/building/REAL300000220154 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220154 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220154/0 /scratch/stefan/7769801/working/building/REAL300000220154 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/155 `/scratch/stefan/7769801/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1) `REAL300000220154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220154 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [27, 15, 15, 15, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 15, 15, 15, 27, 9, 27, 27, 27, 15, 9, 9, 3, 3, 2, 2, 2, 1, 15, 27, 27, 27, 13] 67 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 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: 125 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: REAL300000220154 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 3, 15, 15, 15, 15, 15, 27, 39, 39, 15, 15, 15, 1, 1, 1, 3, 1, 3, 3, 3, 1, 3, 3, 27, 27, 15, 15, 15, 15, 1, 3, 3, 3, 1] 67 rigid atoms, others: [1, 2, 3, 4, 5, 40, 19, 20, 21, 23, 36, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220154 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220154 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220154/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220154 Building REAL300000220155 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220155' /scratch/stefan/7769801/working/building/REAL300000220155 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220155 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220155/0 /scratch/stefan/7769801/working/building/REAL300000220155 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/156 `/scratch/stefan/7769801/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2Br)OCO3)=N1) `REAL300000220155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220155 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2Br)OCO3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'O.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 12, 5, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 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, 19, 31, 31, 31, 19, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 31, 31, 19, 7, 7, 1, 1, 1, 1] 31 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 103 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: REAL300000220155 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2Br)OCO3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'O.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 12, 5, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 1, 11, 11, 19, 19, 19, 19] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 62 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220155 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220155 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220155/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220155 Building REAL300000220156 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220156' /scratch/stefan/7769801/working/building/REAL300000220156 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220156 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220156/0 /scratch/stefan/7769801/working/building/REAL300000220156 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/157 `/scratch/stefan/7769801/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C2C=C1) `REAL300000220156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220156 none COC1=CC2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [33, 17, 17, 17, 17, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 17, 17, 17, 17, 33, 33, 33, 17, 17, 17, 5, 5, 3, 3, 1, 1, 1, 1, 17, 17, 17] 55 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42]) total number of confs: 77 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: REAL300000220156 none COC1=CC2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 33, 55, 55, 17, 17, 17, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 5, 5, 33, 33, 17, 17, 17, 17, 1, 1, 1] 55 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 41, 42, 40, 22, 23, 24, 25, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220156 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220156 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220156/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220156 Building REAL300000220157 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220157' /scratch/stefan/7769801/working/building/REAL300000220157 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220157 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220157/0 /scratch/stefan/7769801/working/building/REAL300000220157 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/158 `/scratch/stefan/7769801/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CS2)=N1) `REAL300000220157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220157 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [26, 26, 26, 26, 39, 39, 39, 26, 26, 26, 12, 12, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 39, 39, 26, 12, 12, 1, 1] 39 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 124 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: REAL300000220157 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 26, 26, 26, 26, 26, 1, 2, 2, 2, 3, 3, 1, 11, 11, 26, 26] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 67 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220157 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220157 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220157/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220157 Building REAL300000220158 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220158' /scratch/stefan/7769801/working/building/REAL300000220158 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220158 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220158/0 /scratch/stefan/7769801/working/building/REAL300000220158 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/159 `/scratch/stefan/7769801/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(=O)[O-])C=C2)=N1) `REAL300000220158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220158 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 38, 65, 65, 24, 24, 24, 4, 4, 1, 1, 1, 1, 1, 1, 7, 27, 43, 43, 1, 1, 24, 24, 24, 24, 38, 38, 24, 4, 4, 1, 1, 27, 27, 1, 1] 201 rigid atoms, others: [33, 34, 37, 38, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 355 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220158 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 13, 13, 24, 24, 13, 13, 77, 161, 167, 167, 24, 24, 1, 2, 2, 2, 3, 3, 1, 13, 13, 24, 24, 161, 161, 24, 24] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 580 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220158 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220158 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220158/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220158 Building REAL300000220159 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220159' /scratch/stefan/7769801/working/building/REAL300000220159 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220159 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220159/0 /scratch/stefan/7769801/working/building/REAL300000220159 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/160 `/scratch/stefan/7769801/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(C)=C1O) `REAL300000220159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220159 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(C)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 9, 9, 9, 5, 5, 9, 9, 9, 9, 5, 5, 3, 3, 2, 2, 2, 1, 9, 9, 9, 9, 18] 30 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 69 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: REAL300000220159 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(C)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 5, 5, 10, 10, 10, 10, 10, 15, 15, 15, 10, 10, 10, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 15, 15, 10, 10, 10, 10, 1, 2, 2, 2, 2] 30 rigid atoms, others: [0, 1, 2, 3, 4, 35, 18, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 63 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220159 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220159 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220159/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220159 Building REAL300000220160 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220160' /scratch/stefan/7769801/working/building/REAL300000220160 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220160 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220160/0 /scratch/stefan/7769801/working/building/REAL300000220160 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/161 `/scratch/stefan/7769801/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C([N+](=O)[O-])=C2)=N1) `REAL300000220160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220160 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 41, 41, 41, 23, 23, 23, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 2, 2, 1, 23, 23, 23, 23, 41, 41, 23, 6, 6, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1] 41 rigid atoms, others: [37, 38, 49, 12, 13, 14, 15, 16, 17, 23, 24, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220160 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 41, 41, 41, 29, 29, 29, 12, 12, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 3, 29, 29, 29, 29, 41, 41, 29, 12, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3] 41 rigid atoms, others: [48, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49]) total number of confs: 129 number of broken/clashed sets: 41 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220160 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 3, 5, 5, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 29, 29, 29, 29, 29, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 3, 1, 7, 7, 23, 23, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 23] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 72 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220160 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220160 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220160/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220160 Building REAL300000220161 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220161' /scratch/stefan/7769801/working/building/REAL300000220161 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220161 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220161/0 /scratch/stefan/7769801/working/building/REAL300000220161 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/162 `/scratch/stefan/7769801/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1O) `REAL300000220161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220161 none COC1=CC(Br)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [60, 40, 40, 40, 40, 40, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 40, 40, 40, 60, 60, 60, 40, 12, 12, 2, 2, 2, 3, 3, 1, 40, 80] 154 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 209 number of broken/clashed sets: 154 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220161 none COC1=CC(Br)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 40, 40, 40, 40, 40, 66, 77, 77, 40, 40, 40, 1, 1, 1, 3, 3, 3, 1, 10, 10, 40, 40, 40, 66, 66, 40, 1, 2] 154 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 263 number of broken/clashed sets: 154 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220161 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220161 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220161/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220161 Building REAL300000220162 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220162' /scratch/stefan/7769801/working/building/REAL300000220162 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220162 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220162/0 /scratch/stefan/7769801/working/building/REAL300000220162 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/163 `/scratch/stefan/7769801/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220162 none CCCOC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 108, 67, 11, 18, 41, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 41, 41, 160, 160, 160, 160, 160, 108, 108, 41, 41, 11, 11, 3, 3, 1, 1, 1, 1, 41, 41] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 693 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: REAL300000220162 none CCCOC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 4, 1, 1, 1, 1, 1, 1, 6, 6, 41, 41, 41, 41, 41, 68, 106, 106, 41, 41, 41, 1, 1, 21, 21, 21, 21, 21, 12, 12, 1, 1, 6, 6, 68, 68, 41, 41, 41, 41, 1, 1] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 42, 22, 23, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 461 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220162 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220162 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220162/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220162 Building REAL300000220163 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220163' /scratch/stefan/7769801/working/building/REAL300000220163 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220163 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220163/0 /scratch/stefan/7769801/working/building/REAL300000220163 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/164 `/scratch/stefan/7769801/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220163 none CC1=NN(CC2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 29, 29, 152, 152, 152, 152, 152, 201, 201, 201, 152, 152, 152, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 29, 29, 152, 152, 152, 201, 201, 152] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 522 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220163 none CC1=NN(CC2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 129, 152, 152, 142, 152, 152, 45, 45, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 45, 45, 45, 129, 129, 152, 152, 152, 152, 152, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 563 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220163 none CC1=NN(CC2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 7, 8, 7, 8, 7, 1, 1, 1, 1, 7, 7, 45, 45, 45, 45, 45, 85, 106, 106, 45, 45, 45, 2, 2, 2, 5, 5, 7, 8, 8, 8, 7, 7, 7, 45, 45, 45, 85, 85, 45] 201 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 414 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220163 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220163 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220163/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220163 Building REAL300000220164 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220164' /scratch/stefan/7769801/working/building/REAL300000220164 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220164 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220164/0 /scratch/stefan/7769801/working/building/REAL300000220164 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/165 `/scratch/stefan/7769801/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC#N) `REAL300000220164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220164 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 33, 33, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 33, 33, 33, 33, 79, 139, 139, 77, 77, 77, 33, 9, 9, 2, 2, 2, 3, 3, 1, 33, 33, 139, 139] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 538 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220164 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 33, 33, 33, 33, 33, 59, 98, 98, 33, 33, 33, 1, 1, 1, 1, 5, 18, 18, 4, 4, 4, 1, 5, 5, 33, 33, 33, 59, 59, 33, 1, 1, 18, 18] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 19, 20, 21, 22, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 418 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220164 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220164 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220164/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220164 Building REAL300000220165 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220165' /scratch/stefan/7769801/working/building/REAL300000220165 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220165 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220165/0 /scratch/stefan/7769801/working/building/REAL300000220165 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/166 `/scratch/stefan/7769801/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC) `REAL300000220165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220165 none CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 60, 47, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 43, 43, 134, 134, 134, 134, 134, 134, 134, 60, 60, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 43, 43, 43, 43, 43] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 553 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220165 none CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 39, 50, 50, 21, 21, 21, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 21, 21, 10, 10, 1, 1, 5, 5, 21, 21, 21, 39, 39, 21, 1, 5, 5, 5, 5, 5] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 47, 23, 24, 25, 38, 5] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52]) total number of confs: 268 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220165 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220165 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220165/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220165 Building REAL300000220166 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220166' /scratch/stefan/7769801/working/building/REAL300000220166 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220166 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220166/0 /scratch/stefan/7769801/working/building/REAL300000220166 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/167 `/scratch/stefan/7769801/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220166 none CC1=NN(C2=CC=CC=C2)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 23, 23, 69, 69, 69, 69, 69, 94, 94, 94, 69, 69, 69, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 94, 94, 69, 69, 69, 69] 94 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 258 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220166 none CC1=NN(C2=CC=CC=C2)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 69, 69, 50, 69, 69, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 50, 50, 50, 69, 69, 50, 69, 69, 50, 50, 50, 12, 12, 3, 3, 2, 2, 2, 1] 94 rigid atoms, others: [45, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 190 number of broken/clashed sets: 13 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220166 none CC1=NN(C2=CC=CC=C2)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 1, 1, 9, 9, 50, 49, 50, 50, 50, 70, 94, 94, 50, 50, 50, 2, 2, 2, 7, 7, 1, 7, 7, 2, 2, 2, 9, 9, 70, 70, 50, 50, 50, 50] 94 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 314 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220166 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220166 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220166/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220166 Building REAL300000220167 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220167' /scratch/stefan/7769801/working/building/REAL300000220167 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220167 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220167/0 /scratch/stefan/7769801/working/building/REAL300000220167 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/168 `/scratch/stefan/7769801/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1OC(F)F) `REAL300000220167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220167 none COC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 54, 54, 54, 54, 54, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 54, 54, 112, 175, 175, 96, 96, 96, 54, 54, 54, 11, 11, 2, 2, 2, 3, 3, 1, 175] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 594 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220167 none COC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 54, 54, 54, 54, 54, 86, 124, 124, 54, 54, 54, 1, 1, 7, 32, 32, 4, 4, 4, 1, 1, 1, 9, 9, 54, 54, 54, 86, 86, 54, 32] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 515 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220167 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220167 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220167/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220167 Building REAL300000220168 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220168' /scratch/stefan/7769801/working/building/REAL300000220168 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220168 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220168/0 /scratch/stefan/7769801/working/building/REAL300000220168 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/169 `/scratch/stefan/7769801/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(C(F)(F)F)=C2)=N1) `REAL300000220168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220168 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 24, 24, 24, 33, 33, 33, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 24, 24, 24, 24, 33, 33, 24, 5, 5, 1, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 94 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220168 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 24, 24, 17, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 3, 1, 9, 9, 24, 24, 23, 24] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 98 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220168 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220168 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220168/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220168 Building REAL300000220169 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220169' /scratch/stefan/7769801/working/building/REAL300000220169 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220169 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220169/0 /scratch/stefan/7769801/working/building/REAL300000220169 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/170 `/scratch/stefan/7769801/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1OC) `REAL300000220169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220169 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 46, 46, 46, 46, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 46, 46, 78, 46, 46, 141, 98, 98, 98, 46, 46, 12, 12, 3, 3, 2, 2, 2, 1, 78, 78, 78, 141, 141, 141] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 364 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: REAL300000220169 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 46, 46, 46, 46, 46, 79, 119, 119, 46, 46, 46, 1, 1, 4, 1, 1, 6, 4, 4, 4, 1, 1, 9, 9, 79, 79, 46, 46, 46, 46, 5, 5, 5, 7, 7, 7] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 23, 24, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 453 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220169 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220169 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220169/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220169 Building REAL300000220170 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220170' /scratch/stefan/7769801/working/building/REAL300000220170 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220170 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220170/0 /scratch/stefan/7769801/working/building/REAL300000220170 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/171 `/scratch/stefan/7769801/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220170 none CCOC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 121, 59, 59, 59, 30, 59, 59, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 164, 164, 164, 164, 164, 59, 59, 59, 59, 13, 12, 3, 3, 2, 2, 2, 1] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 557 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: REAL300000220170 none CCOC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 59, 59, 59, 59, 59, 92, 137, 137, 59, 59, 59, 25, 25, 25, 25, 25, 1, 1, 1, 1, 9, 9, 92, 92, 59, 59, 59, 59] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 526 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220170 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220170 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220170/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220170 Building REAL300000220171 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220171' /scratch/stefan/7769801/working/building/REAL300000220171 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220171 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220171/0 /scratch/stefan/7769801/working/building/REAL300000220171 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/172 `/scratch/stefan/7769801/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220171 none CCOC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [83, 54, 22, 22, 35, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 35, 35, 83, 83, 83, 83, 83, 35, 35, 11, 11, 3, 3, 2, 2, 2, 1, 35, 35] 107 rigid atoms, others: [37, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 340 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: REAL300000220171 none CCOC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [9, 3, 1, 1, 1, 1, 1, 1, 6, 6, 35, 35, 35, 35, 35, 57, 85, 85, 35, 35, 35, 1, 1, 9, 9, 9, 9, 9, 1, 1, 6, 6, 57, 57, 35, 35, 35, 35, 1, 1] 107 rigid atoms, others: [2, 3, 4, 5, 6, 7, 39, 21, 22, 38, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 318 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220171 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220171 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220171/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220171 Building REAL300000220172 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220172' /scratch/stefan/7769801/working/building/REAL300000220172 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220172 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220172/0 /scratch/stefan/7769801/working/building/REAL300000220172 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/173 `/scratch/stefan/7769801/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220172 none COC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [75, 61, 61, 61, 28, 61, 61, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 75, 75, 75, 61, 61, 61, 61, 12, 11, 3, 3, 2, 2, 2, 1] 95 rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 258 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: REAL300000220172 none COC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 61, 61, 61, 61, 61, 89, 95, 95, 61, 61, 61, 4, 4, 4, 1, 1, 1, 1, 12, 12, 89, 89, 61, 61, 61, 61] 95 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 286 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220172 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220172 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220172/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220172 Building REAL300000220173 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220173' /scratch/stefan/7769801/working/building/REAL300000220173 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220173 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220173/0 /scratch/stefan/7769801/working/building/REAL300000220173 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/174 `/scratch/stefan/7769801/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3)C=C2)=N1) `REAL300000220173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220173 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 41, 64, 64, 25, 25, 25, 4, 4, 1, 1, 1, 1, 1, 1, 3, 11, 23, 23, 11, 23, 23, 1, 1, 25, 25, 25, 25, 41, 41, 25, 4, 4, 1, 1, 11, 11, 23, 23, 11, 23, 23, 1, 1] 201 rigid atoms, others: [45, 36, 37, 12, 13, 14, 15, 16, 17, 46, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 296 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220173 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 155, 155, 155, 201, 201, 201, 155, 155, 155, 47, 47, 22, 22, 23, 23, 11, 3, 1, 1, 1, 1, 1, 1, 1, 23, 23, 155, 155, 155, 155, 201, 201, 155, 47, 47, 23, 23, 3, 3, 1, 1, 1, 1, 1, 23, 23] 201 rigid atoms, others: [40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46]) total number of confs: 564 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220173 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 13, 13, 25, 25, 13, 13, 42, 103, 155, 155, 103, 155, 155, 25, 25, 1, 2, 2, 2, 3, 3, 1, 13, 13, 25, 25, 103, 103, 155, 155, 103, 155, 155, 25, 25] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 632 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220173 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220173 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220173/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220173 Building REAL300000220174 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220174' /scratch/stefan/7769801/working/building/REAL300000220174 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220174 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220174/0 /scratch/stefan/7769801/working/building/REAL300000220174 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/175 `/scratch/stefan/7769801/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220174 none COC1=CC=C(Br)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [81, 67, 67, 67, 17, 67, 67, 67, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 81, 81, 81, 67, 67, 67, 11, 11, 2, 2, 2, 3, 3, 1] 103 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 290 number of broken/clashed sets: 103 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220174 none COC1=CC=C(Br)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 67, 67, 67, 67, 67, 97, 103, 103, 67, 67, 67, 4, 4, 4, 1, 1, 1, 11, 11, 67, 67, 67, 97, 97, 67] 103 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 302 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220174 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220174 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220174/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220174 Building REAL300000220175 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220175' /scratch/stefan/7769801/working/building/REAL300000220175 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220175 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220175/0 /scratch/stefan/7769801/working/building/REAL300000220175 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/176 `/scratch/stefan/7769801/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Br)=C1O) `REAL300000220175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220175 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [57, 35, 35, 35, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 35, 35, 35, 35, 35, 57, 57, 57, 35, 10, 10, 2, 2, 2, 3, 3, 1, 35, 70] 152 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 191 number of broken/clashed sets: 152 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220175 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 59, 76, 76, 35, 35, 35, 1, 1, 1, 1, 1, 4, 4, 4, 1, 7, 7, 35, 35, 35, 59, 59, 35, 1, 2] 152 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 36, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 270 number of broken/clashed sets: 152 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220175 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220175 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220175/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220175 Building REAL300000220176 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220176' /scratch/stefan/7769801/working/building/REAL300000220176 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220176 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220176/0 /scratch/stefan/7769801/working/building/REAL300000220176 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/177 `/scratch/stefan/7769801/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C([N+](=O)[O-])=C2)=N1) `REAL300000220176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220176 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [24, 24, 24, 24, 33, 33, 33, 24, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 24, 24, 24, 24, 33, 33, 24, 7, 7, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220176 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 24, 24, 17, 23, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 3, 1, 11, 11, 24, 24, 24] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 99 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220176 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220176 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220176/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220176 Building REAL300000220177 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220177' /scratch/stefan/7769801/working/building/REAL300000220177 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220177 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220177/0 /scratch/stefan/7769801/working/building/REAL300000220177 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/178 `/scratch/stefan/7769801/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)C=C2)N1) `REAL300000220177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220177 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 16, 22, 22, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 10, 10, 10, 10, 16, 16, 4, 4, 1, 1, 3, 3, 1, 3, 3, 1, 1, 10] 22 rigid atoms, others: [33, 34, 40, 41, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 42]) total number of confs: 84 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220177 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 22, 22, 22, 14, 14, 14, 6, 6, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 14, 14, 14, 22, 22, 6, 6, 3, 3, 1, 1, 1, 1, 1, 3, 3, 14] 22 rigid atoms, others: [35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220177 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 6, 6, 10, 10, 6, 6, 14, 14, 8, 14, 14, 10, 10, 1, 2, 2, 2, 3, 3, 6, 6, 10, 10, 14, 14, 10, 14, 14, 10, 10, 1] 22 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 42] set([4, 5, 6, 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, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220177 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220177 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220177/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220177 Building REAL300000220178 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220178' /scratch/stefan/7769801/working/building/REAL300000220178 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220178 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220178/0 /scratch/stefan/7769801/working/building/REAL300000220178 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/179 `/scratch/stefan/7769801/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1O) `REAL300000220178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220178 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 20, 20, 20, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 20, 20, 20, 35, 12, 20, 37, 37, 37, 20, 11, 11, 3, 3, 2, 2, 2, 1, 20, 35, 35, 35, 40] 150 rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41]) 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: REAL300000220178 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 37, 37, 37, 37, 37, 58, 72, 72, 37, 37, 37, 1, 1, 1, 3, 1, 1, 3, 3, 3, 1, 5, 5, 58, 58, 37, 37, 37, 37, 1, 3, 3, 3, 2] 154 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 23, 24, 28, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220178 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220178 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220178/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220178 Building REAL300000220179 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220179' /scratch/stefan/7769801/working/building/REAL300000220179 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220179 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220179/0 /scratch/stefan/7769801/working/building/REAL300000220179 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/180 `/scratch/stefan/7769801/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1O) `REAL300000220179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220179 none CCOC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [171, 131, 41, 41, 41, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 41, 41, 41, 41, 171, 171, 171, 171, 171, 41, 10, 10, 3, 3, 2, 2, 2, 1, 41, 41, 82] 402 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 529 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220179 none CCOC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [30, 7, 1, 1, 1, 1, 1, 5, 5, 41, 41, 41, 41, 41, 72, 119, 119, 41, 41, 41, 1, 1, 1, 1, 30, 30, 30, 30, 30, 1, 5, 5, 72, 72, 41, 41, 41, 41, 1, 1, 2] 402 rigid atoms, others: [2, 3, 4, 5, 6, 39, 20, 21, 22, 23, 38, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 515 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220179 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220179 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220179/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220179 Building REAL300000220180 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220180' /scratch/stefan/7769801/working/building/REAL300000220180 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220180 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220180/0 /scratch/stefan/7769801/working/building/REAL300000220180 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/181 `/scratch/stefan/7769801/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220180 none CSC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [41, 24, 18, 27, 27, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 27, 27, 41, 41, 41, 27, 27, 11, 11, 3, 3, 2, 2, 2, 1, 27, 27] 49 rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 137 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: REAL300000220180 none CSC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 37, 42, 42, 27, 27, 27, 1, 1, 6, 6, 6, 1, 1, 6, 6, 37, 37, 27, 27, 27, 27, 1, 1] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 20, 21, 25, 26, 36] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220180 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220180 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220180/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220180 Building REAL300000220181 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220181' /scratch/stefan/7769801/working/building/REAL300000220181 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220181 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220181/0 /scratch/stefan/7769801/working/building/REAL300000220181 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/182 `/scratch/stefan/7769801/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=CC=C2Cl)=N1) `REAL300000220181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220181 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=CC=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 21, 21, 21, 17, 17, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 21, 17, 4, 4, 1, 1, 1] 21 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 49 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: REAL300000220181 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=CC=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 17, 17, 17, 11, 17, 17, 17, 1, 2, 2, 2, 3, 3, 1, 11, 11, 17, 12, 17] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220181 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220181 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220181/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220181 Building REAL300000220182 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220182' /scratch/stefan/7769801/working/building/REAL300000220182 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220182 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220182/0 /scratch/stefan/7769801/working/building/REAL300000220182 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/183 `/scratch/stefan/7769801/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(OC)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220182 none COC1=CC(OC)=C(OC)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 53, 53, 53, 53, 53, 110, 53, 53, 122, 53, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 79, 79, 79, 53, 110, 110, 110, 122, 122, 122, 53, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 362 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220182 none COC1=CC(OC)=C(OC)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 1, 1, 9, 9, 53, 53, 53, 53, 53, 87, 120, 120, 53, 53, 53, 3, 3, 3, 1, 3, 3, 3, 4, 4, 4, 1, 9, 9, 53, 53, 53, 87, 87, 51] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 10, 11, 12, 36, 29] set([0, 6, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 424 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220182 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220182 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220182/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220182 Building REAL300000220183 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220183' /scratch/stefan/7769801/working/building/REAL300000220183 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220183 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220183/0 /scratch/stefan/7769801/working/building/REAL300000220183 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/184 `/scratch/stefan/7769801/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C)=C1) `REAL300000220183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220183 none CC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 10, 10, 10, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 3, 3, 2, 2, 2, 1, 10, 10, 10, 10] 15 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) 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: REAL300000220183 none CC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 15, 15, 15, 11, 11, 11, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 5, 15, 15, 11, 11, 11, 10, 2, 2, 2, 1] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 20, 21, 22, 26] set([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, 39, 40]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220183 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220183 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220183/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220183 Building REAL300000220184 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220184' /scratch/stefan/7769801/working/building/REAL300000220184 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220184 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220184/0 /scratch/stefan/7769801/working/building/REAL300000220184 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/185 `/scratch/stefan/7769801/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C(F)=C2)N1) `REAL300000220184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220184 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [19, 19, 19, 19, 27, 27, 27, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 27, 27, 6, 6, 1, 1, 1, 19] 27 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 79 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: REAL300000220184 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 9, 9, 19, 19, 19, 1] 27 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 59 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220184 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220184 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220184/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220184 Building REAL300000220185 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220185' /scratch/stefan/7769801/working/building/REAL300000220185 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220185 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220185/0 /scratch/stefan/7769801/working/building/REAL300000220185 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/186 `/scratch/stefan/7769801/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220185 none CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 28, 28, 111, 111, 111, 111, 111, 135, 135, 135, 111, 111, 111, 6, 6, 6, 1, 1, 1, 1, 1, 28, 28, 111, 111, 111, 135, 135, 111] 135 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 306 number of broken/clashed sets: 134 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220185 none CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 111, 111, 61, 111, 111, 61, 61, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 61, 61, 61, 111, 111, 61, 111, 111, 12, 12, 2, 2, 2, 3, 3, 1] 135 rigid atoms, others: [42, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 322 number of broken/clashed sets: 134 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220185 none CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 1, 11, 11, 61, 61, 61, 61, 61, 97, 135, 135, 61, 61, 61, 2, 2, 2, 6, 6, 1, 6, 6, 11, 11, 61, 61, 61, 97, 97, 61] 135 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 467 number of broken/clashed sets: 134 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220185 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220185 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220185/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220185 Building REAL300000220186 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220186' /scratch/stefan/7769801/working/building/REAL300000220186 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220186 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220186/0 /scratch/stefan/7769801/working/building/REAL300000220186 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/187 `/scratch/stefan/7769801/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3)=C2)=N1) `REAL300000220186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220186 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 73, 115, 115, 42, 42, 42, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 2, 6, 6, 1, 42, 42, 42, 42, 73, 73, 42, 5, 5, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 1] 201 rigid atoms, others: [36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 428 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220186 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 201, 201, 201, 148, 148, 148, 25, 25, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 148, 148, 148, 148, 201, 201, 148, 25, 25, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 531 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220186 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 42, 42, 42, 42, 42, 75, 75, 148, 148, 83, 148, 148, 42, 1, 2, 2, 2, 3, 3, 1, 12, 12, 42, 42, 42, 75, 75, 148, 148, 148, 148, 148, 42] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 540 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220186 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220186 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220186/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220186 Building REAL300000220187 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220187' /scratch/stefan/7769801/working/building/REAL300000220187 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220187 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220187/0 /scratch/stefan/7769801/working/building/REAL300000220187 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/188 `/scratch/stefan/7769801/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2Br)=N1) `REAL300000220187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220187 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [17, 17, 17, 17, 30, 30, 30, 17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 30, 30, 17, 7, 7, 1, 1, 1, 1] 30 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 109 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: REAL300000220187 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 17, 17, 9, 17, 17, 17, 1, 2, 2, 2, 3, 3, 1, 9, 9, 17, 17, 17, 17] 30 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 98 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220187 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220187 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220187/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220187 Building REAL300000220188 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220188' /scratch/stefan/7769801/working/building/REAL300000220188 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220188 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220188/0 /scratch/stefan/7769801/working/building/REAL300000220188 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/189 `/scratch/stefan/7769801/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1O) `REAL300000220188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220188 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [39, 25, 25, 25, 25, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 25, 25, 25, 39, 39, 39, 25, 25, 10, 10, 3, 3, 1, 1, 1, 1, 25, 50] 124 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 142 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: REAL300000220188 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 7, 7, 25, 25, 25, 25, 25, 41, 62, 62, 25, 25, 25, 1, 1, 1, 4, 4, 4, 1, 1, 7, 7, 41, 41, 25, 25, 25, 25, 1, 2] 124 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 229 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220188 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220188 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220188/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220188 Building REAL300000220189 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220189' /scratch/stefan/7769801/working/building/REAL300000220189 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220189 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220189/0 /scratch/stefan/7769801/working/building/REAL300000220189 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/190 `/scratch/stefan/7769801/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220189 none COC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [39, 39, 19, 39, 12, 29, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 29, 39, 39, 39, 29, 29, 11, 11, 3, 3, 2, 2, 2, 1, 29, 29] 51 rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 182 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: REAL300000220189 none COC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [6, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 46, 50, 50, 29, 29, 29, 1, 1, 7, 7, 7, 1, 1, 6, 6, 46, 46, 29, 29, 29, 29, 1, 1] 51 rigid atoms, others: [2, 4, 5, 6, 7, 8, 38, 22, 23, 27, 28, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 177 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220189 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220189 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220189/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220189 Building REAL300000220190 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220190' /scratch/stefan/7769801/working/building/REAL300000220190 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220190 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220190/0 /scratch/stefan/7769801/working/building/REAL300000220190 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/191 `/scratch/stefan/7769801/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1) `REAL300000220190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220190 none COC(=O)C1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [13, 13, 1, 13, 1, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 38, 38, 38, 38, 38, 62, 70, 70, 38, 39, 38, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1, 8, 8, 39, 39, 39, 62, 62, 38, 13, 13] 201 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 34, 26] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 286 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220190 none COC(=O)C1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [151, 151, 38, 151, 38, 147, 147, 38, 38, 38, 38, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 38, 147, 147, 151, 151, 151, 147, 147, 38, 39, 11, 11, 2, 2, 2, 3, 3, 1, 147, 147] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 682 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220190 none COC(=O)C1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 13, 13, 13, 13, 38, 38, 147, 147, 147, 147, 147, 201, 201, 201, 147, 147, 147, 13, 1, 1, 6, 6, 6, 1, 1, 13, 13, 38, 38, 147, 147, 147, 201, 201, 147, 1, 1] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 44, 45, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 560 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220190 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220190 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220190/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220190 Building REAL300000220191 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220191' /scratch/stefan/7769801/working/building/REAL300000220191 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220191 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220191/0 /scratch/stefan/7769801/working/building/REAL300000220191 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/192 `/scratch/stefan/7769801/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC4=CC=CC=C43)C=C2)N1) `REAL300000220191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220191 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC4=CC=CC=C43)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 35, 48, 48, 22, 22, 22, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 22, 22, 22, 22, 35, 35, 3, 3, 1, 1, 11, 11, 11, 11, 11, 1, 1, 22] 78 rigid atoms, others: [36, 37, 44, 43, 12, 13, 14, 15, 16, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 45]) total number of confs: 169 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220191 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC4=CC=CC=C43)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 78, 78, 78, 62, 63, 62, 19, 19, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 63, 63, 63, 63, 78, 78, 19, 19, 11, 11, 1, 1, 1, 1, 1, 11, 11, 63] 78 rigid atoms, others: [38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45]) total number of confs: 214 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220191 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC4=CC=CC=C43)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 22, 22, 12, 12, 63, 63, 63, 63, 63, 63, 63, 63, 22, 22, 1, 2, 2, 2, 3, 3, 12, 12, 22, 22, 63, 63, 63, 63, 63, 22, 22, 1] 78 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 45, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220191 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220191 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220191/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220191 Building REAL300000220192 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220192' /scratch/stefan/7769801/working/building/REAL300000220192 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220192 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220192/0 /scratch/stefan/7769801/working/building/REAL300000220192 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/193 `/scratch/stefan/7769801/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)NC3=CC=CC=C32)N1) `REAL300000220192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220192 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)NC3=CC=CC=C32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 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: [43, 43, 43, 43, 51, 51, 51, 42, 43, 43, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 51, 51, 11, 11, 1, 1, 1, 1, 1, 43] 51 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 115 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: REAL300000220192 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)NC3=CC=CC=C32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 2, 2, 2, 3, 3, 11, 11, 43, 43, 43, 43, 43, 1] 51 rigid atoms, others: [0, 1, 2, 3, 36, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220192 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220192 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220192/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220192 Building REAL300000220193 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220193' /scratch/stefan/7769801/working/building/REAL300000220193 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220193 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220193/0 /scratch/stefan/7769801/working/building/REAL300000220193 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/194 `/scratch/stefan/7769801/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCCC3)N=C2)=N1) `REAL300000220193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220193 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 21, 34, 34, 17, 17, 17, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 17, 17, 17, 17, 21, 21, 17, 3, 3, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1] 61 rigid atoms, others: [33, 42, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220193 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 61, 61, 61, 60, 60, 60, 15, 15, 1, 1, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 60, 60, 60, 60, 61, 61, 60, 15, 15, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9] 61 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42]) total number of confs: 115 number of broken/clashed sets: 60 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220193 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 17, 17, 10, 10, 60, 60, 60, 60, 17, 17, 1, 2, 2, 2, 3, 3, 1, 10, 10, 17, 60, 60, 60, 60, 60, 60, 60, 60, 17] 61 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220193 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220193 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220193/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220193 Building REAL300000220194 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220194' /scratch/stefan/7769801/working/building/REAL300000220194 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220194 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220194/0 /scratch/stefan/7769801/working/building/REAL300000220194 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/195 `/scratch/stefan/7769801/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCCOC3=C2)=N1) `REAL300000220194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220194 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 33, 33, 33, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 33, 33, 21, 6, 6, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 106 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220194 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 7, 7, 21, 21, 21, 21, 21, 21] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 58 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220194 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220194 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220194/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220194 Building REAL300000220195 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220195' /scratch/stefan/7769801/working/building/REAL300000220195 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220195 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220195/0 /scratch/stefan/7769801/working/building/REAL300000220195 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/196 `/scratch/stefan/7769801/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)C3=CC=CC=C3S2)N1) `REAL300000220195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220195 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)C3=CC=CC=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 25, 39, 39, 39, 25, 25, 25, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 39, 39, 9, 9, 1, 1, 1, 1, 25] 39 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 127 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: REAL300000220195 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)C3=CC=CC=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 11, 11, 25, 25, 25, 25, 1] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220195 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220195 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220195/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220195 Building REAL300000220196 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220196' /scratch/stefan/7769801/working/building/REAL300000220196 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220196 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220196/0 /scratch/stefan/7769801/working/building/REAL300000220196 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/197 `/scratch/stefan/7769801/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCCCOC3=C2)=N1) `REAL300000220196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220196 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCCCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 12, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 33, 33, 33, 23, 23, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 33, 33, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 32, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 95 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220196 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCCCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 12, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 3, 1, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220196 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220196 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220196/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220196 Building REAL300000220197 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220197' /scratch/stefan/7769801/working/building/REAL300000220197 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220197 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220197/0 /scratch/stefan/7769801/working/building/REAL300000220197 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/198 `/scratch/stefan/7769801/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(F)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220197 none CC1=NN(C2=CC=C(F)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 24, 24, 74, 74, 74, 74, 74, 96, 96, 96, 74, 74, 74, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 24, 24, 74, 74, 74, 96, 96, 74] 96 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 249 number of broken/clashed sets: 95 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220197 none CC1=NN(C2=CC=C(F)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 74, 74, 49, 49, 74, 74, 49, 49, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 49, 49, 49, 74, 74, 74, 74, 49, 49, 49, 11, 11, 2, 2, 2, 3, 3, 1] 96 rigid atoms, others: [45, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 220 number of broken/clashed sets: 95 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220197 none CC1=NN(C2=CC=C(F)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 1, 1, 6, 6, 1, 1, 1, 1, 9, 9, 49, 49, 49, 49, 49, 70, 92, 92, 49, 49, 49, 2, 2, 2, 6, 6, 6, 6, 2, 2, 2, 9, 9, 49, 49, 49, 70, 70, 49] 96 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 306 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220197 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220197 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220197/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220197 Building REAL300000220198 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220198' /scratch/stefan/7769801/working/building/REAL300000220198 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220198 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220198/0 /scratch/stefan/7769801/working/building/REAL300000220198 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/199 `/scratch/stefan/7769801/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=C2)N1) `REAL300000220198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220198 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 28, 28, 28, 39, 39, 39, 28, 28, 28, 6, 6, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 28, 28, 28, 28, 39, 39, 6, 6, 1, 4, 4, 1, 4, 4, 1, 28] 39 rigid atoms, others: [32, 38, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 39]) total number of confs: 116 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220198 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [35, 35, 35, 35, 39, 39, 39, 35, 35, 35, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 39, 39, 12, 12, 4, 1, 1, 1, 1, 1, 4, 35] 39 rigid atoms, others: [33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 83 number of broken/clashed sets: 38 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220198 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 28, 28, 28, 35, 35, 28, 35, 35, 28, 28, 1, 2, 2, 2, 3, 3, 9, 9, 28, 35, 35, 28, 35, 35, 28, 1] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220198 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220198 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220198/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220198 Building REAL300000220199 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220199' /scratch/stefan/7769801/working/building/REAL300000220199 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220199 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220199/0 /scratch/stefan/7769801/working/building/REAL300000220199 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/200 `/scratch/stefan/7769801/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1F) `REAL300000220199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220199 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [37, 24, 23, 24, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 24, 24, 24, 37, 37, 37, 24, 24, 10, 10, 3, 3, 2, 2, 2, 1, 24] 62 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 100 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: REAL300000220199 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 40, 62, 62, 24, 24, 24, 1, 1, 1, 3, 3, 3, 1, 1, 6, 6, 40, 40, 24, 24, 24, 24, 1] 62 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 223 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220199 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220199 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220199/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220199 Building REAL300000220200 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220200' /scratch/stefan/7769801/working/building/REAL300000220200 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220200 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220200/0 /scratch/stefan/7769801/working/building/REAL300000220200 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/201 `/scratch/stefan/7769801/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220200 none COC1=CC=C(C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [77, 63, 63, 63, 41, 63, 63, 63, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 77, 77, 77, 63, 63, 63, 63, 63, 63, 11, 11, 3, 3, 2, 2, 2, 1] 98 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 231 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: REAL300000220200 none COC1=CC=C(C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 63, 63, 63, 63, 63, 92, 98, 98, 63, 63, 63, 4, 4, 4, 1, 1, 2, 2, 2, 1, 11, 11, 92, 92, 63, 63, 63, 63] 98 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 298 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220200 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220200 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220200/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220200 Building REAL300000220201 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220201' /scratch/stefan/7769801/working/building/REAL300000220201 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220201 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220201/0 /scratch/stefan/7769801/working/building/REAL300000220201 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/202 `/scratch/stefan/7769801/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3)N=C2)=N1) `REAL300000220201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220201 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 68, 87, 87, 38, 38, 38, 7, 7, 1, 1, 1, 1, 1, 7, 11, 11, 9, 11, 11, 1, 1, 38, 38, 38, 38, 68, 68, 38, 7, 7, 1, 7, 7, 11, 11, 11, 11, 11, 1] 201 rigid atoms, others: [34, 42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 347 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220201 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 201, 201, 201, 148, 148, 148, 41, 41, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 148, 148, 148, 148, 201, 201, 148, 41, 41, 11, 3, 3, 1, 1, 1, 1, 1, 11] 201 rigid atoms, others: [37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 560 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220201 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 38, 38, 38, 125, 148, 148, 137, 148, 148, 38, 38, 1, 2, 2, 2, 3, 3, 1, 10, 10, 38, 125, 125, 148, 148, 147, 148, 148, 38] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 540 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220201 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220201 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220201/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220201 Building REAL300000220202 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220202' /scratch/stefan/7769801/working/building/REAL300000220202 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220202 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220202/0 /scratch/stefan/7769801/working/building/REAL300000220202 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/203 `/scratch/stefan/7769801/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)S2)=N1) `REAL300000220202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220202 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [48, 48, 48, 48, 61, 63, 63, 48, 48, 48, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 2, 2, 7, 7, 1, 48, 48, 48, 48, 61, 61, 48, 12, 12, 1, 1, 7, 7, 7, 7] 95 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 170 number of broken/clashed sets: 94 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220202 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [79, 79, 79, 79, 95, 95, 95, 79, 79, 79, 37, 37, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 79, 79, 79, 79, 95, 95, 79, 37, 37, 7, 7, 1, 1, 1, 1] 95 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 239 number of broken/clashed sets: 94 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220202 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 48, 48, 48, 48, 79, 79, 73, 74, 79, 79, 48, 1, 2, 2, 2, 3, 3, 1, 11, 11, 48, 48, 79, 79, 79, 79] 95 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 165 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220202 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220202 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220202/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220202 Building REAL300000220203 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220203' /scratch/stefan/7769801/working/building/REAL300000220203 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220203 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220203/0 /scratch/stefan/7769801/working/building/REAL300000220203 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/204 `/scratch/stefan/7769801/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC([N+](=O)[O-])=CC3=C2OCOC3)=N1) `REAL300000220203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220203 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC([N+](=O)[O-])=CC3=C2OCOC3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 5, 12, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 53, 53, 53, 38, 38, 38, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 53, 53, 38, 11, 11, 1, 1, 1, 1, 1, 1] 53 rigid atoms, others: [35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 33, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 148 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: REAL300000220203 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC([N+](=O)[O-])=CC3=C2OCOC3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 5, 12, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 2, 2, 2, 3, 3, 1, 9, 9, 38, 38, 38, 38, 38, 38] 53 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 79 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220203 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220203 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220203/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220203 Building REAL300000220204 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220204' /scratch/stefan/7769801/working/building/REAL300000220204 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220204 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220204/0 /scratch/stefan/7769801/working/building/REAL300000220204 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/205 `/scratch/stefan/7769801/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C2O1) `REAL300000220204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220204 none CCC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [106, 62, 62, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 62, 62, 62, 62, 62, 62, 62, 106, 106, 106, 106, 106, 12, 12, 3, 3, 2, 2, 2, 1, 62, 62, 62, 62] 130 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 347 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: REAL300000220204 none CCC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 11, 11, 62, 61, 62, 62, 62, 90, 99, 99, 62, 62, 62, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 11, 11, 90, 90, 62, 62, 62, 62, 1, 1, 1, 1] 130 rigid atoms, others: [1, 2, 3, 4, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 313 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220204 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220204 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220204/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220204 Building REAL300000220205 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220205' /scratch/stefan/7769801/working/building/REAL300000220205 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220205 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220205/0 /scratch/stefan/7769801/working/building/REAL300000220205 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/206 `/scratch/stefan/7769801/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3F)C=C2)=N1) `REAL300000220205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220205 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 45, 66, 66, 28, 28, 28, 4, 4, 1, 1, 1, 1, 1, 1, 2, 6, 24, 24, 12, 24, 24, 24, 1, 1, 28, 28, 28, 28, 45, 45, 28, 4, 4, 1, 1, 6, 6, 24, 24, 24, 24, 1, 1] 201 rigid atoms, others: [45, 37, 38, 12, 13, 14, 15, 16, 17, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 302 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220205 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 151, 201, 201, 201, 151, 151, 151, 49, 49, 24, 18, 25, 25, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 151, 151, 151, 151, 201, 201, 151, 49, 49, 25, 25, 8, 8, 1, 1, 1, 1, 24, 24] 201 rigid atoms, others: [41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46]) total number of confs: 617 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220205 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 13, 13, 28, 28, 16, 18, 45, 73, 151, 151, 119, 151, 151, 151, 28, 28, 1, 2, 2, 2, 3, 3, 1, 13, 13, 28, 28, 73, 73, 151, 151, 151, 151, 28, 28] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 552 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220205 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220205 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220205/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220205 Building REAL300000220206 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220206' /scratch/stefan/7769801/working/building/REAL300000220206 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220206 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220206/0 /scratch/stefan/7769801/working/building/REAL300000220206 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/207 `/scratch/stefan/7769801/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(C)=O)C1=NC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1) `REAL300000220206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220206 none CCN(C(C)=O)C1=NC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.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, 5, 11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 99, 68, 99, 107, 107, 68, 68, 13, 13, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 68, 68, 167, 167, 167, 167, 167, 107, 107, 107, 13, 13, 2, 2, 2, 3, 3, 1, 68] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 661 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220206 none CCN(C(C)=O)C1=NC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.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, 5, 11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 1, 6, 10, 10, 1, 1, 1, 1, 12, 12, 68, 68, 68, 68, 68, 98, 106, 106, 68, 68, 68, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 68, 68, 68, 98, 98, 64, 1] 201 rigid atoms, others: [2, 6, 7, 8, 9, 41, 23, 24] set([0, 1, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 358 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220206 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220206 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220206/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220206 Building REAL300000220207 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220207' /scratch/stefan/7769801/working/building/REAL300000220207 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220207 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220207/0 /scratch/stefan/7769801/working/building/REAL300000220207 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/208 `/scratch/stefan/7769801/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(F)C=C3)=N2)=N1) `REAL300000220207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220207 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(F)C=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 45, 46, 46, 65, 65, 65, 46, 46, 46, 12, 12, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 45, 46, 46, 46, 65, 65, 44, 12, 12, 1, 3, 3, 3, 3] 65 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 196 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220207 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(F)C=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [53, 53, 53, 53, 65, 65, 65, 53, 53, 53, 22, 22, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 53, 53, 53, 53, 65, 65, 53, 22, 22, 3, 1, 1, 1, 1] 65 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 165 number of broken/clashed sets: 64 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220207 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(F)C=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 46, 46, 46, 46, 53, 53, 46, 46, 53, 53, 46, 1, 2, 2, 2, 3, 3, 1, 11, 11, 46, 53, 53, 53, 53] 65 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220207 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220207 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220207/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220207 Building REAL300000220208 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220208' /scratch/stefan/7769801/working/building/REAL300000220208 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220208 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220208/0 /scratch/stefan/7769801/working/building/REAL300000220208 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/209 `/scratch/stefan/7769801/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC(F)=C3)C=C2)=N1) `REAL300000220208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220208 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC(F)=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 39, 59, 59, 24, 24, 24, 4, 4, 1, 1, 1, 1, 1, 1, 2, 6, 32, 32, 32, 32, 32, 32, 1, 1, 24, 24, 24, 24, 39, 39, 24, 4, 4, 1, 1, 6, 6, 32, 32, 32, 32, 1, 1] 201 rigid atoms, others: [45, 37, 38, 12, 13, 14, 15, 16, 17, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 252 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220208 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC(F)=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 169, 201, 201, 201, 169, 169, 169, 63, 63, 32, 18, 32, 32, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 169, 169, 169, 169, 201, 201, 169, 63, 63, 32, 32, 8, 8, 1, 1, 1, 1, 32, 32] 201 rigid atoms, others: [41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46]) total number of confs: 598 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220208 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC(F)=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 24, 24, 12, 19, 40, 68, 169, 169, 169, 169, 169, 169, 24, 24, 1, 2, 2, 2, 3, 3, 1, 12, 12, 24, 24, 68, 68, 169, 169, 169, 169, 24, 24] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 435 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220208 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220208 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220208/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220208 Building REAL300000220209 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220209' /scratch/stefan/7769801/working/building/REAL300000220209 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220209 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220209/0 /scratch/stefan/7769801/working/building/REAL300000220209 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/210 `/scratch/stefan/7769801/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(NC(=O)C(F)(F)F)=C2)=N1) `REAL300000220209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220209 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(NC(=O)C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 79, 100, 100, 47, 47, 47, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 47, 47, 47, 47, 79, 79, 47, 6, 6, 1, 1, 1, 9, 1] 201 rigid atoms, others: [35, 36, 37, 39, 12, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 353 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220209 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(NC(=O)C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 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 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 47, 47, 47, 47, 47, 146, 146, 146, 146, 146, 146, 47, 1, 2, 2, 2, 3, 3, 1, 12, 12, 47, 47, 47, 146, 47] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 355 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220209 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220209 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220209/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220209 Building REAL300000220210 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220210' /scratch/stefan/7769801/working/building/REAL300000220210 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220210 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220210/0 /scratch/stefan/7769801/working/building/REAL300000220210 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/211 `/scratch/stefan/7769801/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])O2)=N1) `REAL300000220210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220210 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [75, 74, 75, 75, 118, 150, 150, 75, 75, 75, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 7, 7, 1, 74, 75, 75, 75, 118, 118, 75, 13, 13, 1, 1, 7, 7, 2, 7] 185 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 505 number of broken/clashed sets: 184 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220210 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [143, 143, 143, 143, 185, 185, 185, 143, 143, 143, 41, 41, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 143, 143, 143, 143, 185, 185, 143, 41, 41, 7, 7, 1, 1, 1, 1] 185 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 475 number of broken/clashed sets: 184 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220210 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 75, 75, 75, 75, 143, 143, 103, 143, 143, 143, 143, 143, 75, 1, 2, 2, 2, 3, 3, 1, 11, 11, 75, 75, 143, 143, 105, 143] 185 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 348 number of broken/clashed sets: 184 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220210 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220210 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220210/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220210 Building REAL300000220211 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220211' /scratch/stefan/7769801/working/building/REAL300000220211 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220211 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220211/0 /scratch/stefan/7769801/working/building/REAL300000220211 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/212 `/scratch/stefan/7769801/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)C=C1) `REAL300000220211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220211 none COC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 1, 12, 12, 55, 55, 56, 56, 56, 90, 116, 116, 56, 56, 56, 1, 1, 4, 4, 5, 5, 5, 4, 4, 12, 12, 56, 56, 56, 90, 90, 54, 1, 4, 4] 116 rigid atoms, others: [5, 6, 7, 8, 9, 40, 23, 24] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 410 number of broken/clashed sets: 115 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220211 none COC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [92, 86, 85, 92, 92, 56, 56, 56, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 56, 56, 92, 92, 92, 92, 92, 92, 92, 12, 12, 2, 2, 2, 3, 3, 1, 56, 92, 92] 116 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 208 number of broken/clashed sets: 115 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220211 none COC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 34, 34, 92, 92, 92, 92, 92, 116, 116, 116, 92, 92, 92, 4, 4, 1, 1, 2, 2, 2, 1, 1, 34, 34, 92, 92, 92, 116, 116, 90, 4, 1, 1] 116 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 304 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220211 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220211 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220211/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220211 Building REAL300000220212 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220212' /scratch/stefan/7769801/working/building/REAL300000220212 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220212 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220212/0 /scratch/stefan/7769801/working/building/REAL300000220212 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/213 `/scratch/stefan/7769801/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(Cl)=C1) `REAL300000220212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220212 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [37, 25, 19, 31, 31, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 31, 31, 31, 37, 37, 37, 31, 31, 12, 12, 3, 3, 2, 2, 2, 1, 31] 61 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 134 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: REAL300000220212 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [2, 1, 1, 1, 1, 1, 1, 9, 9, 31, 31, 31, 31, 31, 49, 61, 61, 31, 31, 31, 1, 1, 1, 3, 3, 3, 1, 1, 9, 9, 49, 49, 31, 31, 31, 31, 1] 61 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 211 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220212 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220212 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220212/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220212 Building REAL300000220213 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220213' /scratch/stefan/7769801/working/building/REAL300000220213 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220213 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220213/0 /scratch/stefan/7769801/working/building/REAL300000220213 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/214 `/scratch/stefan/7769801/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1O) `REAL300000220213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220213 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [44, 30, 30, 30, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 30, 30, 30, 30, 44, 44, 44, 30, 12, 12, 3, 3, 2, 2, 2, 1, 30, 30, 60] 116 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 164 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: REAL300000220213 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 1, 1, 1, 1, 6, 6, 30, 30, 30, 30, 30, 45, 58, 58, 30, 30, 30, 1, 1, 1, 1, 3, 3, 3, 1, 6, 6, 45, 45, 30, 30, 30, 30, 1, 1, 2] 116 rigid atoms, others: [1, 2, 3, 4, 5, 35, 19, 20, 21, 22, 36, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 37]) total number of confs: 190 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220213 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220213 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220213/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220213 Building REAL300000220214 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220214' /scratch/stefan/7769801/working/building/REAL300000220214 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220214 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220214/0 /scratch/stefan/7769801/working/building/REAL300000220214 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/215 `/scratch/stefan/7769801/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(Cl)=C2)N1) `REAL300000220214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220214 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [18, 18, 18, 18, 27, 27, 27, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 27, 27, 6, 6, 1, 1, 1, 1, 18] 27 rigid atoms, others: [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, 32, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 83 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: REAL300000220214 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 8, 8, 18, 18, 16, 18, 18, 18, 1, 2, 2, 2, 3, 3, 8, 8, 18, 18, 17, 18, 1] 27 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 20] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 63 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220214 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220214 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220214/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220214 Building REAL300000220215 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220215' /scratch/stefan/7769801/working/building/REAL300000220215 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220215 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220215/0 /scratch/stefan/7769801/working/building/REAL300000220215 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/216 `/scratch/stefan/7769801/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C=C2)=N1) `REAL300000220215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220215 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 31, 49, 49, 17, 17, 17, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 17, 17, 17, 17, 31, 31, 17, 3, 3, 1, 1, 10, 10, 10, 11, 10, 10, 10, 10, 10, 10, 1, 1] 63 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 46, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 189 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220215 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 52, 52, 52, 63, 63, 63, 52, 52, 52, 17, 17, 1, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 52, 52, 52, 52, 63, 63, 52, 17, 17, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 63 rigid atoms, others: [45, 36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47]) total number of confs: 171 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220215 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 17, 17, 11, 11, 52, 52, 52, 52, 52, 17, 17, 1, 2, 2, 2, 3, 3, 1, 11, 11, 17, 17, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 17, 17] 63 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220215 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220215 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220215/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220215 Building REAL300000220216 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220216' /scratch/stefan/7769801/working/building/REAL300000220216 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220216 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220216/0 /scratch/stefan/7769801/working/building/REAL300000220216 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/217 `/scratch/stefan/7769801/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(F)C=C3)O2)=N1) `REAL300000220216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220216 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(F)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [61, 60, 61, 61, 90, 120, 120, 61, 61, 61, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 2, 4, 7, 7, 1, 60, 61, 61, 61, 90, 90, 61, 13, 13, 1, 1, 7, 7, 7, 7] 120 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 400 number of broken/clashed sets: 119 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220216 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(F)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 120, 120, 120, 95, 95, 95, 42, 42, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 95, 95, 95, 95, 120, 120, 95, 42, 42, 7, 7, 1, 1, 1, 1] 120 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 313 number of broken/clashed sets: 119 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220216 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(F)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 61, 61, 61, 61, 95, 95, 85, 95, 95, 95, 61, 1, 2, 2, 2, 3, 3, 1, 12, 12, 61, 61, 95, 95, 95, 95] 120 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 225 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220216 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220216 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220216/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220216 Building REAL300000220217 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220217' /scratch/stefan/7769801/working/building/REAL300000220217 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220217 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220217/0 /scratch/stefan/7769801/working/building/REAL300000220217 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/218 `/scratch/stefan/7769801/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3Cl)N=C2)=N1) `REAL300000220217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220217 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3Cl)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 42, 48, 48, 27, 27, 27, 6, 6, 1, 1, 1, 1, 1, 7, 11, 11, 9, 11, 11, 11, 1, 1, 27, 27, 27, 27, 42, 42, 27, 6, 6, 1, 7, 7, 11, 11, 11, 11, 1] 201 rigid atoms, others: [35, 42, 12, 13, 14, 15, 16, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220217 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3Cl)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 138, 138, 138, 201, 201, 201, 138, 138, 138, 38, 38, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 138, 138, 138, 138, 201, 201, 138, 38, 38, 11, 5, 5, 1, 1, 1, 1, 11] 201 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 611 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220217 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3Cl)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 78, 138, 138, 111, 138, 138, 138, 27, 27, 1, 2, 2, 2, 3, 3, 1, 9, 9, 27, 78, 78, 138, 138, 138, 138, 27] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 515 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220217 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220217 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220217/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220217 Building REAL300000220218 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220218' /scratch/stefan/7769801/working/building/REAL300000220218 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220218 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220218/0 /scratch/stefan/7769801/working/building/REAL300000220218 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/219 `/scratch/stefan/7769801/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C(=NC(C)=C2C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1) `REAL300000220218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220218 none CC1=CN2C(=NC(C)=C2C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [35, 31, 35, 35, 35, 35, 35, 35, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 12, 12, 2, 2, 2, 3, 3, 1] 49 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 95 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: REAL300000220218 none CC1=CN2C(=NC(C)=C2C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 1, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 49, 49, 49, 35, 35, 35, 1, 2, 2, 2, 1, 2, 2, 2, 7, 7, 35, 35, 35, 49, 49, 35] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220218 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220218 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220218/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220218 Building REAL300000220219 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220219' /scratch/stefan/7769801/working/building/REAL300000220219 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220219 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220219/0 /scratch/stefan/7769801/working/building/REAL300000220219 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/220 `/scratch/stefan/7769801/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OC(F)(F)F)=N1) `REAL300000220219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220219 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 61, 79, 79, 43, 43, 43, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 43, 43, 43, 43, 61, 61, 43, 7, 7, 1, 1, 1, 1] 81 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 278 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220219 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 43, 43, 19, 43, 43, 43, 67, 74, 74, 74, 1, 2, 2, 2, 3, 3, 1, 12, 12, 43, 43, 43, 43] 81 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 265 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220219 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220219 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220219/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220219 Building REAL300000220220 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220220' /scratch/stefan/7769801/working/building/REAL300000220220 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220220 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220220/0 /scratch/stefan/7769801/working/building/REAL300000220220 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/221 `/scratch/stefan/7769801/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SC(F)(F)F)C=C2)=N1) `REAL300000220220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220220 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SC(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 23, 23, 37, 53, 53, 23, 23, 23, 4, 4, 1, 1, 1, 1, 1, 1, 12, 22, 22, 22, 1, 1, 23, 23, 23, 23, 37, 37, 23, 4, 4, 1, 1, 1, 1] 101 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 242 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220220 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SC(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 23, 23, 23, 23, 66, 67, 67, 67, 23, 23, 1, 2, 2, 2, 3, 3, 1, 12, 12, 23, 23, 23, 23] 101 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 137 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220220 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220220 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220220/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220220 Building REAL300000220221 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220221' /scratch/stefan/7769801/working/building/REAL300000220221 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220221 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220221/0 /scratch/stefan/7769801/working/building/REAL300000220221 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/222 `/scratch/stefan/7769801/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=NC=C3)C=C2)=N1) `REAL300000220221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220221 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=NC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 39, 59, 59, 23, 23, 23, 4, 4, 1, 1, 1, 1, 1, 1, 4, 12, 28, 28, 12, 28, 28, 1, 1, 23, 23, 23, 23, 39, 39, 23, 4, 4, 1, 1, 12, 12, 28, 28, 28, 28, 1, 1] 201 rigid atoms, others: [45, 36, 37, 44, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 291 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220221 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=NC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 152, 152, 152, 201, 201, 201, 152, 152, 152, 50, 50, 25, 25, 28, 28, 15, 5, 1, 1, 1, 1, 1, 1, 1, 28, 28, 152, 152, 152, 152, 201, 201, 152, 50, 50, 28, 28, 5, 5, 1, 1, 1, 1, 28, 28] 201 rigid atoms, others: [40, 41, 42, 43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45]) total number of confs: 582 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220221 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=NC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 23, 23, 12, 12, 39, 100, 152, 152, 100, 152, 151, 23, 23, 1, 2, 2, 2, 3, 3, 1, 12, 12, 23, 23, 101, 101, 152, 152, 152, 152, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 621 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220221 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220221 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220221/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220221 Building REAL300000220222 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220222' /scratch/stefan/7769801/working/building/REAL300000220222 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220222 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220222/0 /scratch/stefan/7769801/working/building/REAL300000220222 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/223 `/scratch/stefan/7769801/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])S2)=N1) `REAL300000220222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220222 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 92, 106, 106, 67, 67, 67, 13, 13, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 67, 67, 67, 67, 92, 92, 67, 13, 13, 1, 1, 5, 5, 5, 5] 120 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 304 number of broken/clashed sets: 119 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220222 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 120, 120, 120, 99, 99, 99, 37, 37, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 99, 99, 99, 99, 120, 120, 99, 37, 37, 5, 5, 1, 1, 1, 1] 120 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 293 number of broken/clashed sets: 119 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220222 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 67, 99, 99, 99, 99, 99, 99, 99, 99, 67, 1, 2, 2, 2, 3, 3, 1, 12, 12, 67, 67, 99, 99, 99, 99] 120 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 172 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220222 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220222 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220222/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220222 Building REAL300000220223 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220223' /scratch/stefan/7769801/working/building/REAL300000220223 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220223 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220223/0 /scratch/stefan/7769801/working/building/REAL300000220223 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/224 `/scratch/stefan/7769801/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(O)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220223 none COC1=CC(O)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [60, 49, 49, 49, 19, 49, 49, 49, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 60, 60, 60, 49, 98, 49, 49, 12, 12, 3, 3, 2, 2, 2, 1] 150 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 316 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: REAL300000220223 none COC1=CC(O)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 49, 49, 49, 49, 49, 67, 75, 75, 49, 49, 49, 3, 3, 3, 1, 2, 1, 1, 11, 11, 67, 67, 49, 49, 49, 49] 150 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 28, 29] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 213 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220223 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220223 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220223/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220223 Building REAL300000220224 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220224' /scratch/stefan/7769801/working/building/REAL300000220224 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220224 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220224/0 /scratch/stefan/7769801/working/building/REAL300000220224 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/225 `/scratch/stefan/7769801/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC2=C1OCCO2) `REAL300000220224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220224 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [39, 28, 28, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 39, 39, 39, 28, 11, 11, 2, 2, 2, 3, 3, 1, 28, 28, 28, 28, 28] 65 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 94 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: REAL300000220224 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 49, 65, 65, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 6, 6, 28, 28, 28, 49, 49, 28, 1, 1, 1, 1, 1] 65 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 234 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220224 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220224 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220224/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220224 Building REAL300000220225 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220225' /scratch/stefan/7769801/working/building/REAL300000220225 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220225 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220225/0 /scratch/stefan/7769801/working/building/REAL300000220225 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/226 `/scratch/stefan/7769801/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(F)C=CC=C2F)N1) `REAL300000220225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220225 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(F)C=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [14, 14, 14, 14, 22, 22, 22, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 22, 5, 5, 1, 1, 1, 14] 22 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 71 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: REAL300000220225 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(F)C=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 3, 3, 11, 11, 16, 16, 16, 1] 22 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220225 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220225 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220225/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220225 Building REAL300000220226 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220226' /scratch/stefan/7769801/working/building/REAL300000220226 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220226 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220226/0 /scratch/stefan/7769801/working/building/REAL300000220226 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/227 `/scratch/stefan/7769801/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=CO1) `REAL300000220226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220226 none COC(=O)C1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 164, 79, 165, 79, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 79, 79, 79, 165, 165, 165, 12, 12, 2, 2, 2, 3, 3, 1, 79, 79] 201 rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 402 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220226 none COC(=O)C1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 11, 11, 79, 79, 79, 79, 79, 130, 167, 167, 79, 79, 79, 1, 1, 1, 13, 13, 13, 11, 11, 79, 79, 79, 130, 130, 79, 1, 1] 201 rigid atoms, others: [2, 35, 4, 5, 6, 34, 20, 21, 22] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 584 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220226 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220226 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220226/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220226 Building REAL300000220227 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220227' /scratch/stefan/7769801/working/building/REAL300000220227 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220227 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220227/0 /scratch/stefan/7769801/working/building/REAL300000220227 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/228 `/scratch/stefan/7769801/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(C)N1C1CCCCC1) `REAL300000220227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220227 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(C)N1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 43, 43, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 43, 43, 43, 43, 61, 61, 61, 61, 61, 43, 43, 43, 43, 12, 12, 2, 2, 2, 3, 3, 1, 43, 43, 43, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61] 89 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220227 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(C)N1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 21, 21, 61, 61, 61, 61, 61, 89, 89, 89, 61, 61, 61, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 21, 21, 61, 61, 61, 89, 89, 61, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 89 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 268 number of broken/clashed sets: 89 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220227 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(C)N1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 43, 43, 43, 43, 43, 61, 71, 71, 43, 43, 43, 1, 1, 1, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 12, 12, 43, 43, 43, 61, 61, 43, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 89 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 231 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220227 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220227 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220227/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220227 Building REAL300000220228 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220228' /scratch/stefan/7769801/working/building/REAL300000220228 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220228 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220228/0 /scratch/stefan/7769801/working/building/REAL300000220228 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/229 `/scratch/stefan/7769801/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C2=C(C=CC=C2)C2=C1C=CC(C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)=C2) `REAL300000220228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220228 none CCN1C2=C(C=CC=C2)C2=C1C=CC(C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)=C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [45, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 26, 45, 45, 45, 45, 45, 26, 26, 26, 26, 26, 26, 10, 10, 3, 3, 2, 2, 2, 1, 26] 65 rigid atoms, others: [47, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48]) total number of confs: 183 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: REAL300000220228 none CCN1C2=C(C=CC=C2)C2=C1C=CC(C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)=C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 49, 65, 65, 26, 26, 26, 1, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 49, 49, 26, 26, 26, 26, 1] 65 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 34, 35, 36, 37, 38, 39, 48] set([0, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 253 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220228 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220228 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220228/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220228 Building REAL300000220229 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220229' /scratch/stefan/7769801/working/building/REAL300000220229 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220229 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220229/0 /scratch/stefan/7769801/working/building/REAL300000220229 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/230 `/scratch/stefan/7769801/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(COC2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=C2)C=C1) `REAL300000220229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220229 none CC1=CC=C(COC2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 37, 37, 37, 37, 37, 63, 79, 79, 37, 37, 37, 1, 1, 14, 14, 15, 15, 15, 14, 14, 5, 5, 1, 1, 5, 5, 37, 37, 37, 63, 63, 37, 1, 1, 14, 14] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 46, 47, 25, 26, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 333 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220229 none CC1=CC=C(COC2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 136, 155, 155, 110, 37, 37, 37, 37, 37, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 37, 37, 155, 155, 155, 155, 155, 155, 155, 110, 110, 37, 37, 12, 12, 2, 2, 2, 3, 3, 1, 37, 37, 155, 155] 201 rigid atoms, others: [45, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 571 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220229 none CC1=CC=C(COC2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 59, 59, 154, 154, 154, 154, 154, 201, 201, 201, 154, 154, 154, 17, 17, 1, 1, 2, 2, 2, 1, 1, 7, 7, 17, 17, 59, 59, 154, 154, 154, 201, 201, 154, 17, 17, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 48, 49, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 577 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220229 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220229 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220229/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220229 Building REAL300000220230 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220230' /scratch/stefan/7769801/working/building/REAL300000220230 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220230 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220230/0 /scratch/stefan/7769801/working/building/REAL300000220230 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/231 `/scratch/stefan/7769801/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)C=C2)=N1) `REAL300000220230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220230 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 15, 15, 15, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 10, 10, 10, 15, 15, 10, 4, 4, 1, 1, 1, 1] 15 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 53 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: REAL300000220230 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 3, 3, 1, 7, 7, 10, 10, 10, 10] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 44 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220230 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220230 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220230/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220230 Building REAL300000220231 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220231' /scratch/stefan/7769801/working/building/REAL300000220231 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220231 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220231/0 /scratch/stefan/7769801/working/building/REAL300000220231 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/232 `/scratch/stefan/7769801/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)C(=O)N(C)C2=O)=N1) `REAL300000220231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220231 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)C(=O)N(C)C2=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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: [37, 37, 37, 37, 49, 49, 49, 37, 37, 37, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 49, 49, 37, 10, 10, 1, 2, 2, 2, 1, 1, 1] 49 rigid atoms, others: [32, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 134 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: REAL300000220231 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)C(=O)N(C)C2=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 37, 37, 37, 37, 25, 37, 37, 37, 37, 1, 2, 2, 2, 3, 3, 1, 11, 11, 37, 37, 37, 37, 37, 37, 37] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220231 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220231 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220231/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220231 Building REAL300000220232 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220232' /scratch/stefan/7769801/working/building/REAL300000220232 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220232 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220232/0 /scratch/stefan/7769801/working/building/REAL300000220232 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/233 `/scratch/stefan/7769801/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220232 none CC1=NN(C)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 41, 41, 41, 41, 41, 41, 12, 12, 2, 2, 2, 3, 3, 1] 51 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 87 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: REAL300000220232 none CC1=NN(C)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 41, 41, 41, 41, 41, 51, 51, 51, 41, 41, 41, 2, 2, 2, 2, 2, 2, 11, 11, 41, 41, 41, 51, 51, 41] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 133 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220232 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220232 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220232/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220232 Building REAL300000220233 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220233' /scratch/stefan/7769801/working/building/REAL300000220233 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220233 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220233/0 /scratch/stefan/7769801/working/building/REAL300000220233 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/234 `/scratch/stefan/7769801/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(O)C=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220233 none COC1=C(O)C=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [72, 56, 56, 56, 56, 56, 56, 56, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 72, 72, 72, 112, 56, 56, 56, 11, 11, 3, 3, 2, 2, 2, 1] 184 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 246 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: REAL300000220233 none COC1=C(O)C=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 56, 56, 56, 56, 56, 83, 92, 92, 56, 56, 56, 5, 5, 5, 2, 1, 1, 1, 11, 11, 83, 83, 56, 56, 56, 55] 184 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([0, 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]) total number of confs: 290 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220233 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220233 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220233/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220233 Building REAL300000220234 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220234' /scratch/stefan/7769801/working/building/REAL300000220234 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220234 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220234/0 /scratch/stefan/7769801/working/building/REAL300000220234 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/235 `/scratch/stefan/7769801/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220234 none COC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 61, 61, 61, 61, 61, 105, 160, 160, 61, 61, 61, 11, 11, 11, 11, 11, 11, 11, 1, 1, 11, 11, 105, 105, 62, 62, 62, 61, 11, 11] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 33] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 601 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220234 none COC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 94, 90, 133, 133, 62, 61, 61, 61, 61, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 133, 133, 133, 133, 133, 133, 133, 61, 61, 11, 11, 3, 3, 2, 2, 2, 1, 133, 133] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 388 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220234 none COC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 52, 52, 133, 133, 133, 133, 133, 201, 201, 201, 133, 133, 133, 1, 1, 2, 2, 2, 1, 1, 11, 11, 52, 52, 201, 201, 133, 133, 133, 133, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 43, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 638 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220234 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220234 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220234/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220234 Building REAL300000220235 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220235' /scratch/stefan/7769801/working/building/REAL300000220235 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220235 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220235/0 /scratch/stefan/7769801/working/building/REAL300000220235 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/236 `/scratch/stefan/7769801/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220235 none CC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 87, 87, 87, 87, 87, 134, 163, 163, 87, 88, 87, 7, 7, 7, 7, 7, 7, 7, 1, 1, 11, 11, 134, 134, 88, 88, 88, 87, 7, 7] 164 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 527 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220235 none CC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [126, 119, 126, 126, 88, 87, 87, 87, 87, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 126, 126, 126, 126, 126, 126, 126, 87, 87, 12, 12, 3, 3, 2, 2, 2, 1, 126, 126] 164 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 237 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220235 none CC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 40, 40, 126, 126, 126, 126, 126, 164, 164, 164, 126, 126, 126, 1, 1, 2, 2, 2, 1, 1, 8, 8, 40, 40, 164, 164, 126, 126, 126, 126, 1, 1] 164 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 42, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 437 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220235 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220235 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220235/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220235 Building REAL300000220236 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220236' /scratch/stefan/7769801/working/building/REAL300000220236 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220236 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220236/0 /scratch/stefan/7769801/working/building/REAL300000220236 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/237 `/scratch/stefan/7769801/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC3=CC=CC=C23)N1) `REAL300000220236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220236 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [41, 41, 41, 41, 51, 51, 51, 41, 41, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 51, 51, 11, 11, 1, 1, 1, 1, 1, 41] 51 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 122 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: REAL300000220236 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 3, 3, 11, 11, 41, 41, 41, 41, 41, 1] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220236 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220236 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220236/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220236 Building REAL300000220237 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220237' /scratch/stefan/7769801/working/building/REAL300000220237 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220237 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220237/0 /scratch/stefan/7769801/working/building/REAL300000220237 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/238 `/scratch/stefan/7769801/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C) `REAL300000220237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220237 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [40, 11, 11, 29, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 29, 29, 40, 40, 40, 29, 29, 11, 11, 3, 3, 1, 1, 1, 1, 29, 29, 29, 29] 59 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 138 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: REAL300000220237 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 50, 59, 59, 29, 29, 29, 1, 1, 1, 4, 4, 4, 1, 1, 6, 6, 50, 50, 29, 29, 29, 29, 1, 2, 2, 2] 59 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 217 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220237 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220237 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220237/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220237 Building REAL300000220238 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220238' /scratch/stefan/7769801/working/building/REAL300000220238 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220238 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220238/0 /scratch/stefan/7769801/working/building/REAL300000220238 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/239 `/scratch/stefan/7769801/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N=C3C(=C2)C=NN3C(C)C)=N1) `REAL300000220238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220238 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N=C3C(=C2)C=NN3C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [67, 67, 67, 67, 101, 120, 120, 67, 67, 67, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 67, 101, 101, 67, 9, 9, 1, 1, 12, 13, 13, 13, 13, 13, 13] 133 rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 413 number of broken/clashed sets: 133 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220238 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N=C3C(=C2)C=NN3C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 103, 103, 1, 2, 2, 2, 3, 3, 1, 12, 12, 67, 67, 103, 103, 103, 103, 103, 103, 103] 133 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 310 number of broken/clashed sets: 133 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220238 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220238 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220238/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220238 Building REAL300000220239 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220239' /scratch/stefan/7769801/working/building/REAL300000220239 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220239 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220239/0 /scratch/stefan/7769801/working/building/REAL300000220239 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/240 `/scratch/stefan/7769801/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=CC(Cl)=C2Cl)=N1) `REAL300000220239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220239 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=CC(Cl)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [41, 41, 41, 41, 49, 49, 49, 41, 41, 41, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 49, 49, 41, 7, 7, 1, 1] 49 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 103 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: REAL300000220239 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=CC(Cl)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 3, 3, 1, 11, 11, 41, 41] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 86 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220239 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220239 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220239/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220239 Building REAL300000220240 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220240' /scratch/stefan/7769801/working/building/REAL300000220240 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220240 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220240/0 /scratch/stefan/7769801/working/building/REAL300000220240 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/241 `/scratch/stefan/7769801/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=C(F)C=C3)S2)N1) `REAL300000220240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220240 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=C(F)C=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [44, 44, 44, 44, 53, 55, 55, 44, 44, 44, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 3, 2, 7, 7, 1, 44, 44, 44, 44, 53, 53, 12, 12, 1, 1, 7, 7, 7, 7, 44] 93 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 145 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220240 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=C(F)C=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [82, 82, 82, 82, 93, 93, 93, 82, 82, 82, 45, 45, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 82, 82, 82, 82, 93, 93, 45, 45, 7, 7, 1, 1, 1, 1, 82] 93 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 219 number of broken/clashed sets: 92 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220240 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=C(F)C=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 44, 44, 44, 44, 82, 82, 74, 75, 82, 82, 44, 1, 2, 2, 2, 3, 3, 11, 11, 44, 44, 82, 82, 82, 82, 1] 93 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 39] set([4, 5, 6, 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: 184 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220240 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220240 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220240/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220240 Building REAL300000220241 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220241' /scratch/stefan/7769801/working/building/REAL300000220241 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220241 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220241/0 /scratch/stefan/7769801/working/building/REAL300000220241 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/242 `/scratch/stefan/7769801/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CC=N2)=N1) `REAL300000220241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220241 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CC=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 36, 58, 58, 28, 28, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 54, 54, 54, 54, 54, 28, 28, 28, 28, 36, 36, 28, 7, 7, 1, 1, 1, 1, 23, 23, 54, 54, 54, 54] 201 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45]) total number of confs: 289 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220241 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CC=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 177, 201, 201, 201, 177, 177, 177, 102, 102, 54, 54, 54, 40, 54, 54, 31, 7, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 201, 201, 177, 102, 102, 54, 54, 54, 54, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 581 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220241 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CC=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 28, 28, 20, 28, 28, 28, 59, 137, 177, 177, 177, 177, 177, 1, 2, 2, 2, 3, 3, 1, 9, 9, 28, 28, 28, 28, 137, 137, 177, 177, 177, 177] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 568 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220241 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220241 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220241/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220241 Building REAL300000220242 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220242' /scratch/stefan/7769801/working/building/REAL300000220242 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220242 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220242/0 /scratch/stefan/7769801/working/building/REAL300000220242 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/243 `/scratch/stefan/7769801/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)S2)=N1) `REAL300000220242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220242 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [26, 26, 26, 26, 31, 31, 31, 26, 26, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 31, 31, 26, 9, 9, 1, 1] 31 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 73 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: REAL300000220242 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 26, 26, 26, 26, 26, 1, 2, 2, 2, 3, 3, 1, 9, 9, 26, 26] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 68 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220242 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220242 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220242/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220242 Building REAL300000220243 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220243' /scratch/stefan/7769801/working/building/REAL300000220243 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220243 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220243/0 /scratch/stefan/7769801/working/building/REAL300000220243 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/244 `/scratch/stefan/7769801/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CSC=N2)=N1) `REAL300000220243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220243 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CSC=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 52, 82, 82, 36, 36, 36, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 44, 44, 44, 44, 36, 36, 36, 36, 52, 52, 36, 9, 9, 1, 1, 1, 1, 23, 23, 44, 44] 201 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 368 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220243 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CSC=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 162, 201, 201, 201, 162, 162, 162, 88, 88, 44, 44, 44, 37, 44, 44, 22, 5, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 201, 201, 162, 88, 88, 44, 44, 44, 44, 5, 5, 1, 1] 201 rigid atoms, others: [41, 42, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 580 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220243 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CSC=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 36, 36, 20, 36, 36, 36, 57, 136, 162, 162, 162, 162, 1, 2, 2, 2, 3, 3, 1, 9, 9, 36, 36, 36, 36, 136, 136, 162, 162] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 558 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220243 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220243 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220243/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220243 Building REAL300000220244 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220244' /scratch/stefan/7769801/working/building/REAL300000220244 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220244 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220244/0 /scratch/stefan/7769801/working/building/REAL300000220244 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/245 `/scratch/stefan/7769801/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CC=N3)C=C2)N1) `REAL300000220244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220244 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CC=N3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 13, 13, 13, 13, 25, 25, 3, 3, 1, 1, 3, 3, 3, 1, 1, 13] 25 rigid atoms, others: [32, 33, 37, 38, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39]) total number of confs: 99 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220244 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CC=N3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 25, 25, 25, 25, 25, 25, 25, 5, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 25, 25, 25, 25, 25, 25, 5, 5, 3, 3, 1, 1, 1, 3, 3, 25] 25 rigid atoms, others: [34, 35, 36, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 50 number of broken/clashed sets: 25 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220244 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CC=N3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 3, 3, 1, 1, 1, 1, 1, 9, 9, 13, 13, 9, 9, 25, 25, 25, 25, 13, 13, 1, 2, 2, 2, 3, 3, 9, 9, 13, 13, 25, 25, 25, 13, 13, 1] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 76 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220244 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220244 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220244/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220244 Building REAL300000220245 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220245' /scratch/stefan/7769801/working/building/REAL300000220245 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220245 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220245/0 /scratch/stefan/7769801/working/building/REAL300000220245 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/246 `/scratch/stefan/7769801/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)S2)=N1) `REAL300000220245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220245 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 77, 83, 83, 53, 53, 53, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 7, 7, 1, 53, 53, 53, 53, 77, 77, 53, 12, 12, 1, 1, 7, 7, 7, 7] 112 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 261 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220245 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 112, 112, 112, 84, 84, 84, 38, 38, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 84, 84, 84, 84, 112, 112, 84, 38, 38, 7, 7, 1, 1, 1, 1] 112 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 322 number of broken/clashed sets: 111 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220245 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 53, 53, 53, 53, 84, 84, 80, 84, 84, 84, 84, 84, 53, 1, 2, 2, 2, 3, 3, 1, 12, 12, 53, 53, 84, 84, 84, 84] 112 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 175 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220245 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220245 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220245/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220245 Building REAL300000220246 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220246' /scratch/stefan/7769801/working/building/REAL300000220246 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220246 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220246/0 /scratch/stefan/7769801/working/building/REAL300000220246 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/247 `/scratch/stefan/7769801/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)S2)=N1) `REAL300000220246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220246 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [55, 55, 55, 55, 89, 102, 102, 55, 55, 55, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 1, 55, 55, 55, 55, 89, 89, 55, 12, 11, 1, 1, 7, 7, 2, 7] 138 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 352 number of broken/clashed sets: 137 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220246 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [111, 111, 111, 111, 138, 138, 138, 111, 111, 111, 47, 47, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 111, 111, 111, 111, 138, 138, 111, 47, 47, 7, 7, 1, 1, 1, 1] 138 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 359 number of broken/clashed sets: 137 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220246 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 55, 55, 55, 55, 111, 111, 92, 111, 111, 111, 55, 1, 2, 2, 2, 3, 3, 1, 11, 11, 55, 55, 111, 111, 95, 111] 138 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 255 number of broken/clashed sets: 137 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220246 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220246 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220246/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220246 Building REAL300000220247 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220247' /scratch/stefan/7769801/working/building/REAL300000220247 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220247 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220247/0 /scratch/stefan/7769801/working/building/REAL300000220247 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/248 `/scratch/stefan/7769801/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)S2)=N1) `REAL300000220247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220247 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [50, 50, 50, 50, 74, 103, 103, 51, 51, 51, 9, 9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 1, 50, 51, 51, 51, 74, 74, 51, 10, 9, 1, 1, 12, 12, 12, 12] 201 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 351 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220247 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [170, 170, 170, 170, 201, 201, 201, 170, 170, 170, 65, 65, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 170, 170, 170, 170, 201, 201, 170, 65, 65, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 475 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220247 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 170, 170, 170, 170, 170, 170, 170, 170, 50, 1, 2, 2, 2, 3, 3, 1, 9, 9, 50, 50, 170, 170, 170, 170] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 245 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220247 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220247 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220247/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220247 Building REAL300000220248 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220248' /scratch/stefan/7769801/working/building/REAL300000220248 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220248 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220248/0 /scratch/stefan/7769801/working/building/REAL300000220248 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/249 `/scratch/stefan/7769801/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)S2)N1) `REAL300000220248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220248 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 69, 69, 69, 99, 109, 109, 69, 69, 69, 11, 11, 1, 1, 1, 1, 1, 1, 13, 13, 1, 13, 13, 13, 1, 69, 70, 70, 70, 99, 99, 11, 11, 1, 1, 13, 13, 10, 13, 70] 201 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 350 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220248 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 156, 201, 201, 201, 156, 156, 156, 86, 86, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 156, 156, 156, 156, 201, 201, 86, 86, 13, 13, 1, 1, 1, 1, 156] 201 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 558 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220248 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 69, 69, 69, 69, 156, 156, 74, 156, 156, 156, 69, 1, 2, 2, 2, 3, 3, 11, 11, 69, 69, 156, 156, 154, 156, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 39] set([4, 5, 6, 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: 491 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220248 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220248 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220248/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220248 Building REAL300000220249 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220249' /scratch/stefan/7769801/working/building/REAL300000220249 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220249 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220249/0 /scratch/stefan/7769801/working/building/REAL300000220249 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/250 `/scratch/stefan/7769801/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220249 none CNC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [39, 39, 21, 39, 11, 34, 34, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 34, 34, 39, 39, 39, 39, 34, 34, 11, 11, 3, 3, 2, 2, 2, 1, 34, 34] 49 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 207 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: REAL300000220249 none CNC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [4, 4, 1, 4, 1, 1, 1, 1, 1, 6, 6, 34, 34, 34, 34, 34, 49, 49, 49, 34, 34, 34, 1, 1, 4, 4, 4, 4, 1, 1, 6, 6, 49, 49, 34, 34, 34, 34, 1, 1] 49 rigid atoms, others: [2, 4, 5, 6, 7, 8, 39, 22, 23, 38, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 145 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220249 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220249 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220249/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220249 Building REAL300000220250 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220250' /scratch/stefan/7769801/working/building/REAL300000220250 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220250 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220250/0 /scratch/stefan/7769801/working/building/REAL300000220250 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/251 `/scratch/stefan/7769801/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(Br)=C2)=N1) `REAL300000220250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220250 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [23, 23, 23, 23, 29, 29, 29, 23, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 29, 29, 23, 7, 7, 1, 1] 29 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 73 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: REAL300000220250 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 3, 1, 9, 9, 23, 23] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 62 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220250 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220250 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220250/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220250 Building REAL300000220251 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220251' /scratch/stefan/7769801/working/building/REAL300000220251 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220251 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220251/0 /scratch/stefan/7769801/working/building/REAL300000220251 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/252 `/scratch/stefan/7769801/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC(Cl)=C3)S2)=N1) `REAL300000220251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220251 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC(Cl)=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 64, 94, 106, 106, 64, 64, 64, 11, 11, 1, 1, 1, 1, 1, 1, 12, 12, 11, 12, 12, 12, 1, 64, 64, 64, 64, 94, 94, 64, 11, 11, 1, 1, 12, 12, 11, 12] 201 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 330 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220251 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC(Cl)=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 172, 201, 201, 201, 172, 172, 172, 72, 72, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 172, 172, 172, 172, 201, 201, 172, 72, 72, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 470 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220251 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC(Cl)=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 64, 64, 64, 64, 172, 172, 172, 172, 172, 172, 64, 1, 2, 2, 2, 3, 3, 1, 11, 11, 64, 64, 172, 172, 172, 172] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 258 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220251 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220251 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220251/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220251 Building REAL300000220252 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220252' /scratch/stefan/7769801/working/building/REAL300000220252 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220252 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220252/0 /scratch/stefan/7769801/working/building/REAL300000220252 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/253 `/scratch/stefan/7769801/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCCC(=O)[O-])C=C2)=N1) `REAL300000220252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220252 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCCC(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 35, 56, 56, 21, 21, 21, 3, 3, 1, 1, 1, 1, 1, 1, 7, 11, 31, 37, 37, 1, 1, 21, 21, 21, 21, 35, 35, 21, 3, 3, 1, 1, 11, 11, 31, 31, 1, 1] 201 rigid atoms, others: [34, 35, 40, 41, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 340 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220252 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCCC(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 21, 21, 12, 12, 89, 107, 157, 162, 162, 21, 21, 1, 2, 2, 2, 3, 3, 1, 12, 12, 21, 21, 107, 107, 157, 157, 21, 21] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 583 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220252 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220252 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220252/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220252 Building REAL300000220253 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220253' /scratch/stefan/7769801/working/building/REAL300000220253 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220253 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220253/0 /scratch/stefan/7769801/working/building/REAL300000220253 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/254 `/scratch/stefan/7769801/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC(C3=CC=CC=N3)=N2)N1) `REAL300000220253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220253 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC(C3=CC=CC=N3)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [63, 63, 63, 63, 93, 123, 123, 62, 63, 62, 13, 13, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 63, 63, 63, 63, 93, 93, 13, 13, 1, 12, 12, 12, 12, 63] 160 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 398 number of broken/clashed sets: 159 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220253 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC(C3=CC=CC=N3)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [133, 133, 133, 133, 160, 160, 160, 133, 133, 133, 55, 55, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 133, 133, 133, 133, 160, 160, 55, 55, 12, 1, 1, 1, 1, 133] 160 rigid atoms, others: [33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 401 number of broken/clashed sets: 159 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220253 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC(C3=CC=CC=N3)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 63, 63, 63, 63, 133, 133, 133, 133, 133, 63, 1, 2, 2, 2, 3, 3, 11, 11, 63, 133, 133, 133, 133, 1] 160 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 209 number of broken/clashed sets: 159 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220253 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220253 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220253/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220253 Building REAL300000220254 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220254' /scratch/stefan/7769801/working/building/REAL300000220254 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220254 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220254/0 /scratch/stefan/7769801/working/building/REAL300000220254 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/255 `/scratch/stefan/7769801/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3CCCC3)C=C2)N1) `REAL300000220254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220254 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3CCCC3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 16, 16, 26, 28, 28, 16, 16, 16, 4, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 16, 16, 16, 16, 26, 26, 4, 4, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 16] 51 rigid atoms, others: [32, 33, 42, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 98 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220254 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3CCCC3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 39, 39, 39, 51, 51, 51, 39, 39, 39, 11, 11, 1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 39, 39, 39, 39, 51, 51, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 39] 51 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 51 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220254 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3CCCC3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 16, 16, 11, 13, 39, 39, 39, 39, 16, 16, 1, 2, 2, 2, 3, 3, 11, 11, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 16, 16, 1] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 44, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220254 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220254 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220254/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220254 Building REAL300000220255 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220255' /scratch/stefan/7769801/working/building/REAL300000220255 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220255 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220255/0 /scratch/stefan/7769801/working/building/REAL300000220255 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/256 `/scratch/stefan/7769801/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220255 none CCCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 131, 131, 131, 131, 54, 54, 13, 13, 23, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 23, 23, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 54, 54, 23, 23, 8, 8, 2, 2, 2, 3, 3, 1, 23, 23] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 52, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 498 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220255 none CCCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 23, 23, 23, 23, 23, 41, 56, 56, 23, 23, 23, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 1, 5, 5, 23, 23, 23, 41, 41, 23, 1, 1] 201 rigid atoms, others: [11, 7, 8, 9, 10, 43, 44, 12, 53, 54, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 232 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220255 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220255 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220255/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220255 Building REAL300000220256 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220256' /scratch/stefan/7769801/working/building/REAL300000220256 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220256 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220256/0 /scratch/stefan/7769801/working/building/REAL300000220256 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/257 `/scratch/stefan/7769801/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=CC=C2F)N1) `REAL300000220256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220256 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [28, 28, 28, 28, 44, 44, 44, 28, 28, 28, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 44, 44, 9, 9, 1, 1, 1, 28] 44 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 140 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: REAL300000220256 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 28, 28, 28, 28, 28, 28, 28, 1, 2, 2, 2, 3, 3, 11, 11, 28, 28, 28, 1] 44 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220256 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220256 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220256/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220256 Building REAL300000220257 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220257' /scratch/stefan/7769801/working/building/REAL300000220257 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220257 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220257/0 /scratch/stefan/7769801/working/building/REAL300000220257 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/258 `/scratch/stefan/7769801/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(OC(C)C)C=C2)N1) `REAL300000220257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220257 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(OC(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 27, 27, 27, 44, 72, 72, 27, 27, 27, 4, 4, 1, 1, 1, 1, 1, 1, 13, 35, 35, 1, 1, 27, 27, 27, 27, 44, 44, 4, 4, 1, 1, 35, 35, 35, 35, 35, 35, 35, 1, 1, 27] 140 rigid atoms, others: [32, 40, 41, 12, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 354 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220257 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(OC(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 27, 27, 12, 12, 95, 116, 116, 27, 27, 1, 2, 2, 2, 3, 3, 12, 12, 27, 27, 116, 116, 116, 116, 116, 116, 116, 27, 27, 1] 140 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 42] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 336 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220257 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220257 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220257/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220257 Building REAL300000220258 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220258' /scratch/stefan/7769801/working/building/REAL300000220258 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220258 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220258/0 /scratch/stefan/7769801/working/building/REAL300000220258 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/259 `/scratch/stefan/7769801/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C12) `REAL300000220258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220258 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [82, 55, 55, 55, 55, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 55, 55, 55, 55, 55, 55, 82, 82, 82, 55, 55, 12, 12, 3, 3, 2, 2, 2, 1, 55, 55, 55, 55] 96 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 157 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: REAL300000220258 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 10, 10, 55, 55, 55, 55, 55, 84, 96, 96, 55, 55, 55, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 10, 10, 84, 84, 55, 55, 55, 55, 1, 1, 1, 1] 96 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 41, 42, 20, 21, 22, 23, 24, 25, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 305 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220258 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220258 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220258/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220258 Building REAL300000220259 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220259' /scratch/stefan/7769801/working/building/REAL300000220259 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220259 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220259/0 /scratch/stefan/7769801/working/building/REAL300000220259 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/260 `/scratch/stefan/7769801/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CN=C2)=N1) `REAL300000220259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220259 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CN=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 37, 62, 62, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 25, 56, 56, 56, 56, 56, 31, 31, 31, 31, 37, 37, 31, 7, 7, 1, 1, 1, 1, 25, 25, 56, 56, 56, 56] 201 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45]) total number of confs: 300 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220259 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CN=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 178, 201, 201, 201, 178, 178, 178, 93, 93, 56, 56, 56, 56, 56, 56, 33, 7, 1, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 201, 201, 178, 93, 93, 56, 56, 56, 56, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 503 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220259 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CN=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 31, 31, 19, 31, 31, 31, 55, 151, 178, 178, 178, 178, 178, 1, 2, 2, 2, 3, 3, 1, 9, 9, 31, 31, 31, 31, 151, 151, 178, 178, 178, 178] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 603 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220259 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220259 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220259/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220259 Building REAL300000220260 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220260' /scratch/stefan/7769801/working/building/REAL300000220260 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220260 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220260/0 /scratch/stefan/7769801/working/building/REAL300000220260 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/261 `/scratch/stefan/7769801/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OC(F)F)=N1) `REAL300000220260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220260 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OC(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 97, 139, 139, 59, 59, 59, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 39, 39, 59, 59, 59, 59, 97, 97, 59, 9, 9, 1, 1, 1, 39] 201 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 596 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220260 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OC(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 59, 59, 59, 17, 59, 59, 59, 140, 185, 185, 1, 2, 2, 2, 3, 3, 1, 11, 11, 59, 59, 59, 185] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 611 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220260 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220260 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220260/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220260 Building REAL300000220261 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220261' /scratch/stefan/7769801/working/building/REAL300000220261 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220261 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220261/0 /scratch/stefan/7769801/working/building/REAL300000220261 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/262 `/scratch/stefan/7769801/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2N2C=NC=N2)N1) `REAL300000220261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220261 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2N2C=NC=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 101, 130, 130, 56, 56, 56, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 56, 56, 56, 56, 101, 101, 9, 9, 1, 1, 1, 1, 10, 10, 55] 163 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 470 number of broken/clashed sets: 162 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220261 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2N2C=NC=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 163, 163, 163, 105, 105, 105, 35, 35, 10, 10, 10, 9, 10, 10, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 163, 163, 35, 35, 10, 10, 10, 10, 1, 1, 105] 163 rigid atoms, others: [36, 37, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 525 number of broken/clashed sets: 162 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220261 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2N2C=NC=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 56, 56, 24, 56, 56, 56, 105, 105, 105, 105, 1, 2, 2, 2, 3, 3, 12, 12, 56, 56, 56, 56, 105, 105, 1] 163 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 313 number of broken/clashed sets: 162 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220261 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220261 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220261/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220261 Building REAL300000220262 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220262' /scratch/stefan/7769801/working/building/REAL300000220262 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220262 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220262/0 /scratch/stefan/7769801/working/building/REAL300000220262 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/263 `/scratch/stefan/7769801/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)O2)C=C1) `REAL300000220262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220262 none CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 67, 67, 93, 117, 117, 67, 67, 67, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 12, 12, 93, 93, 68, 68, 68, 67, 7, 7] 122 rigid atoms, others: [4, 5, 6, 7, 8, 9, 32, 23, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 383 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220262 none CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 103, 103, 67, 67, 67, 67, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 67, 103, 103, 103, 103, 103, 103, 103, 67, 68, 11, 11, 3, 3, 2, 2, 2, 1, 103, 103] 122 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 413 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220262 none CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 57, 57, 106, 106, 106, 106, 106, 122, 122, 122, 106, 106, 106, 8, 1, 1, 2, 2, 2, 1, 1, 8, 8, 57, 57, 122, 122, 106, 106, 106, 106, 1, 1] 122 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 42, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 298 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220262 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220262 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220262/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220262 Building REAL300000220263 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220263' /scratch/stefan/7769801/working/building/REAL300000220263 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220263 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220263/0 /scratch/stefan/7769801/working/building/REAL300000220263 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/264 `/scratch/stefan/7769801/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC(F)(F)F)=C2)=N1) `REAL300000220263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220263 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 60, 74, 74, 37, 37, 37, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 1, 37, 37, 37, 37, 60, 60, 37, 6, 6, 1, 1, 1, 15, 15, 1] 201 rigid atoms, others: [34, 35, 36, 39, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 290 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220263 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 37, 37, 37, 37, 37, 106, 141, 141, 141, 141, 37, 1, 2, 2, 2, 3, 3, 1, 10, 10, 37, 37, 37, 141, 141, 37] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 375 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220263 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220263 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220263/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220263 Building REAL300000220264 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220264' /scratch/stefan/7769801/working/building/REAL300000220264 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220264 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220264/0 /scratch/stefan/7769801/working/building/REAL300000220264 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/265 `/scratch/stefan/7769801/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCO3)N1) `REAL300000220264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220264 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCO3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [38, 38, 38, 38, 50, 50, 50, 38, 38, 38, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 50, 50, 12, 12, 1, 1, 1, 1, 1, 38] 50 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 131 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: REAL300000220264 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCO3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 38, 38, 38, 38, 38, 38, 38, 38, 1, 2, 2, 2, 3, 3, 11, 11, 38, 38, 38, 38, 38, 1] 50 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220264 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220264 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220264/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220264 Building REAL300000220265 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220265' /scratch/stefan/7769801/working/building/REAL300000220265 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220265 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220265/0 /scratch/stefan/7769801/working/building/REAL300000220265 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/266 `/scratch/stefan/7769801/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(Cl)C=C3)N=C2)=N1) `REAL300000220265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220265 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(Cl)C=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 27, 27, 39, 39, 39, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 4, 1, 1, 27, 27, 27, 27, 39, 39, 27, 7, 7, 1, 4, 4, 4, 4, 1] 39 rigid atoms, others: [34, 39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 124 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220265 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(Cl)C=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 39, 39, 39, 31, 31, 31, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 31, 31, 31, 31, 39, 39, 31, 10, 10, 4, 1, 1, 1, 1, 4] 39 rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 98 number of broken/clashed sets: 38 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220265 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(Cl)C=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 27, 27, 27, 31, 31, 27, 31, 31, 31, 27, 27, 1, 2, 2, 2, 3, 3, 1, 10, 10, 27, 31, 31, 31, 31, 27] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 97 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220265 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220265 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220265/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220265 Building REAL300000220266 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220266' /scratch/stefan/7769801/working/building/REAL300000220266 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220266 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220266/0 /scratch/stefan/7769801/working/building/REAL300000220266 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/267 `/scratch/stefan/7769801/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220266 none CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 117, 48, 48, 48, 48, 48, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 48, 159, 159, 159, 159, 159, 48, 48, 48, 12, 12, 3, 3, 2, 2, 2, 1, 48] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 434 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: REAL300000220266 none CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 48, 48, 48, 48, 48, 80, 114, 114, 48, 48, 48, 1, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 80, 80, 48, 48, 48, 48, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 39, 22, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 446 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220266 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220266 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220266/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220266 Building REAL300000220267 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220267' /scratch/stefan/7769801/working/building/REAL300000220267 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220267 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220267/0 /scratch/stefan/7769801/working/building/REAL300000220267 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/268 `/scratch/stefan/7769801/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC([N+](=O)[O-])=C2)=N1) `REAL300000220267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220267 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [22, 22, 22, 22, 33, 33, 33, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 22, 22, 22, 33, 33, 22, 6, 6, 1, 1] 33 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 105 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: REAL300000220267 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 3, 6, 6, 1, 1, 1, 1, 1, 8, 8, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 1, 8, 8, 22, 22] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 63 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220267 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220267 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220267/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220267 Building REAL300000220268 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220268' /scratch/stefan/7769801/working/building/REAL300000220268 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220268 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220268/0 /scratch/stefan/7769801/working/building/REAL300000220268 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/269 `/scratch/stefan/7769801/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220268 none COC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 11, 10, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 34, 34, 34, 33, 33, 63, 100, 100, 34, 34, 34, 11, 15, 15, 15, 10, 11, 11, 1, 1, 11, 11, 63, 63, 34, 34, 34, 34, 11] 201 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 403 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220268 none COC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 90, 90, 90, 90, 90, 34, 34, 34, 34, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 90, 118, 118, 118, 90, 90, 90, 33, 34, 8, 8, 3, 3, 2, 2, 2, 1, 90] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43]) total number of confs: 207 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220268 none COC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 36, 36, 90, 90, 90, 90, 90, 158, 201, 201, 90, 90, 90, 1, 3, 3, 3, 1, 1, 1, 11, 11, 36, 36, 158, 158, 90, 90, 90, 90, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 43, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220268 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220268 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220268/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220268 Building REAL300000220269 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220269' /scratch/stefan/7769801/working/building/REAL300000220269 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220269 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220269/0 /scratch/stefan/7769801/working/building/REAL300000220269 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/270 `/scratch/stefan/7769801/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220269 none COCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 120, 106, 104, 29, 29, 29, 29, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 131, 131, 131, 120, 120, 106, 106, 29, 29, 29, 9, 9, 2, 2, 2, 3, 3, 1, 29] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43]) total number of confs: 279 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220269 none COCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 7, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 54, 78, 78, 29, 29, 29, 1, 24, 24, 24, 12, 12, 7, 7, 1, 1, 1, 5, 5, 29, 29, 29, 54, 54, 29, 1] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 43, 24] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 339 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220269 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220269 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220269/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220269 Building REAL300000220270 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220270' /scratch/stefan/7769801/working/building/REAL300000220270 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220270 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220270/0 /scratch/stefan/7769801/working/building/REAL300000220270 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/271 `/scratch/stefan/7769801/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCOCC3)N=C2)=N1) `REAL300000220270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220270 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCOCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 31, 49, 49, 19, 19, 19, 3, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 1, 19, 19, 19, 19, 31, 31, 19, 3, 3, 1, 13, 13, 12, 13, 12, 13, 13, 13, 1] 67 rigid atoms, others: [34, 43, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 189 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220270 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCOCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 67, 67, 67, 60, 60, 60, 21, 21, 2, 2, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 60, 60, 60, 60, 67, 67, 60, 21, 21, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13] 67 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43]) total number of confs: 167 number of broken/clashed sets: 66 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220270 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCOCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 19, 19, 9, 9, 60, 60, 60, 60, 60, 19, 19, 1, 2, 2, 2, 3, 3, 1, 9, 9, 19, 60, 60, 60, 60, 60, 60, 60, 60, 19] 67 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 153 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220270 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220270 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220270/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220270 Building REAL300000220271 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220271' /scratch/stefan/7769801/working/building/REAL300000220271 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220271 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220271/0 /scratch/stefan/7769801/working/building/REAL300000220271 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/272 `/scratch/stefan/7769801/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)N=C2)N1) `REAL300000220271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220271 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [14, 14, 14, 14, 21, 32, 32, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 14, 14, 14, 14, 21, 21, 3, 3, 1, 7, 7, 1, 7, 7, 1, 14] 32 rigid atoms, others: [33, 39, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 40]) total number of confs: 127 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220271 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 32, 32, 32, 31, 31, 31, 11, 11, 1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 31, 31, 31, 32, 32, 11, 11, 7, 1, 1, 1, 1, 1, 7, 31] 32 rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 74 number of broken/clashed sets: 31 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220271 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 9, 9, 29, 29, 11, 29, 29, 13, 13, 1, 2, 2, 2, 3, 3, 9, 9, 13, 29, 29, 11, 29, 29, 13, 1] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 40, 25] set([4, 5, 6, 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, 39]) total number of confs: 128 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220271 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220271 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220271/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220271 Building REAL300000220272 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220272' /scratch/stefan/7769801/working/building/REAL300000220272 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220272 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220272/0 /scratch/stefan/7769801/working/building/REAL300000220272 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/273 `/scratch/stefan/7769801/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCCCO3)N1) `REAL300000220272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220272 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCCCO3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 50, 50, 50, 35, 35, 35, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 41, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 144 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: REAL300000220272 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCCCO3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1] 50 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 41, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 79 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220272 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220272 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220272/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220272 Building REAL300000220273 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220273' /scratch/stefan/7769801/working/building/REAL300000220273 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220273 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220273/0 /scratch/stefan/7769801/working/building/REAL300000220273 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/274 `/scratch/stefan/7769801/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Cl)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220273 none COC1=CC=C(Cl)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [77, 63, 63, 63, 11, 63, 63, 63, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 77, 77, 77, 63, 63, 63, 11, 11, 3, 3, 2, 2, 2, 1] 98 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 278 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: REAL300000220273 none COC1=CC=C(Cl)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 63, 63, 63, 63, 63, 92, 98, 98, 63, 63, 63, 4, 4, 4, 1, 1, 1, 11, 11, 92, 92, 63, 63, 63, 63] 98 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 292 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220273 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220273 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220273/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220273 Building REAL300000220274 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220274' /scratch/stefan/7769801/working/building/REAL300000220274 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220274 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220274/0 /scratch/stefan/7769801/working/building/REAL300000220274 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/275 `/scratch/stefan/7769801/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(Cl)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220274 none CC1=NN(C2=CC=C(Cl)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 24, 24, 73, 73, 73, 73, 73, 98, 98, 98, 73, 73, 73, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 24, 24, 73, 73, 73, 98, 98, 73] 98 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 267 number of broken/clashed sets: 97 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220274 none CC1=NN(C2=CC=C(Cl)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 43, 73, 73, 67, 67, 73, 73, 43, 43, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 43, 43, 43, 73, 73, 73, 73, 43, 43, 43, 12, 12, 2, 2, 2, 3, 3, 1] 98 rigid atoms, others: [45, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 97 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220274 none CC1=NN(C2=CC=C(Cl)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 6, 6, 2, 2, 6, 6, 1, 1, 1, 1, 9, 9, 43, 43, 43, 43, 43, 67, 94, 94, 43, 43, 43, 2, 2, 2, 6, 6, 6, 6, 2, 2, 2, 9, 9, 43, 43, 43, 67, 67, 43] 98 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 336 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220274 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220274 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220274/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220274 Building REAL300000220275 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220275' /scratch/stefan/7769801/working/building/REAL300000220275 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220275 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220275/0 /scratch/stefan/7769801/working/building/REAL300000220275 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/276 `/scratch/stefan/7769801/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220275 none CCCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 68, 68, 20, 20, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 20, 133, 133, 133, 133, 133, 68, 68, 20, 20, 20, 7, 7, 3, 3, 1, 1, 1, 1, 20] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 475 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: REAL300000220275 none CCCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 20, 20, 20, 20, 20, 36, 68, 68, 20, 20, 20, 1, 13, 13, 13, 13, 13, 5, 5, 1, 1, 1, 5, 5, 36, 36, 20, 20, 20, 20, 1] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 42, 23, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 295 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220275 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220275 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220275/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220275 Building REAL300000220276 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220276' /scratch/stefan/7769801/working/building/REAL300000220276 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220276 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220276/0 /scratch/stefan/7769801/working/building/REAL300000220276 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/277 `/scratch/stefan/7769801/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCCC3=C2)N1) `REAL300000220276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220276 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [19, 19, 19, 19, 26, 26, 26, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 26, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 19] 26 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 37]) total number of confs: 73 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: REAL300000220276 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 9, 9, 19, 19, 19, 19, 19, 19, 19, 1] 26 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 59 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220276 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220276 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220276/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220276 Building REAL300000220277 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220277' /scratch/stefan/7769801/working/building/REAL300000220277 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220277 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220277/0 /scratch/stefan/7769801/working/building/REAL300000220277 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/278 `/scratch/stefan/7769801/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CS3)C=C2F)N1) `REAL300000220277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220277 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CS3)C=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 95, 110, 110, 65, 65, 65, 12, 12, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 1, 65, 65, 65, 65, 95, 95, 12, 12, 1, 1, 13, 13, 13, 1, 65] 175 rigid atoms, others: [33, 34, 38, 12, 13, 14, 15, 16, 17, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 39]) total number of confs: 342 number of broken/clashed sets: 175 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220277 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CS3)C=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 175, 175, 175, 155, 155, 155, 79, 79, 12, 12, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 13, 155, 155, 155, 155, 175, 175, 79, 79, 13, 13, 1, 1, 1, 13, 155] 175 rigid atoms, others: [35, 36, 37, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 416 number of broken/clashed sets: 175 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220277 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CS3)C=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 65, 65, 65, 65, 155, 155, 155, 155, 65, 65, 65, 1, 2, 2, 2, 3, 3, 11, 11, 65, 65, 155, 155, 155, 65, 1] 175 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 39] set([4, 5, 6, 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: 246 number of broken/clashed sets: 175 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220277 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220277 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220277/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220277 Building REAL300000220278 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220278' /scratch/stefan/7769801/working/building/REAL300000220278 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220278 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220278/0 /scratch/stefan/7769801/working/building/REAL300000220278 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/279 `/scratch/stefan/7769801/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCCO3)N1) `REAL300000220278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220278 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCCO3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 4, 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: [35, 35, 35, 35, 47, 47, 47, 35, 35, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 47, 47, 11, 11, 1, 1, 1, 1, 1, 1, 1, 35] 47 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 128 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220278 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCCO3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 10, 10, 35, 35, 35, 35, 35, 35, 35, 1] 47 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220278 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220278 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220278/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220278 Building REAL300000220279 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220279' /scratch/stefan/7769801/working/building/REAL300000220279 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220279 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220279/0 /scratch/stefan/7769801/working/building/REAL300000220279 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/280 `/scratch/stefan/7769801/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C3=CC=CC=C3)=CS2)N1) `REAL300000220279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220279 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C3=CC=CC=C3)=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [64, 64, 64, 64, 88, 97, 97, 63, 64, 63, 12, 12, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 64, 64, 64, 64, 88, 88, 12, 12, 1, 3, 3, 2, 3, 3, 1, 64] 97 rigid atoms, others: [32, 38, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 39]) total number of confs: 280 number of broken/clashed sets: 96 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220279 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C3=CC=CC=C3)=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [78, 78, 78, 78, 97, 97, 97, 78, 78, 78, 23, 23, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 78, 78, 78, 78, 97, 97, 23, 23, 3, 1, 1, 1, 1, 1, 3, 78] 97 rigid atoms, others: [33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 239 number of broken/clashed sets: 96 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220279 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C3=CC=CC=C3)=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 64, 64, 64, 78, 78, 64, 78, 78, 64, 64, 1, 2, 2, 2, 3, 3, 11, 11, 64, 78, 78, 64, 78, 78, 64, 1] 97 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 183 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220279 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220279 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220279/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220279 Building REAL300000220280 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220280' /scratch/stefan/7769801/working/building/REAL300000220280 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220280 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220280/0 /scratch/stefan/7769801/working/building/REAL300000220280 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/281 `/scratch/stefan/7769801/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2=CC=CC=C2)N1) `REAL300000220280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220280 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 83, 85, 85, 53, 53, 53, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 53, 53, 53, 53, 83, 83, 9, 9, 1, 1, 1, 1, 4, 4, 4, 4, 4, 53] 85 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 270 number of broken/clashed sets: 85 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220280 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 85, 85, 85, 61, 61, 61, 19, 19, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 85, 85, 19, 19, 4, 4, 4, 4, 1, 1, 1, 1, 1, 61] 85 rigid atoms, others: [37, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 243 number of broken/clashed sets: 85 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220280 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 53, 53, 53, 53, 53, 53, 61, 61, 57, 61, 61, 1, 2, 2, 2, 3, 3, 11, 11, 53, 53, 53, 53, 61, 61, 61, 61, 61, 1] 85 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 42] set([4, 5, 6, 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, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220280 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220280 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220280/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220280 Building REAL300000220281 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220281' /scratch/stefan/7769801/working/building/REAL300000220281 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220281 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220281/0 /scratch/stefan/7769801/working/building/REAL300000220281 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/282 `/scratch/stefan/7769801/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CC=C3)=C2)N1) `REAL300000220281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220281 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CC=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 53, 71, 71, 30, 30, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 30, 30, 30, 30, 53, 53, 6, 6, 1, 1, 1, 3, 3, 1, 3, 3, 1, 30] 71 rigid atoms, others: [33, 34, 35, 41, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 42]) total number of confs: 258 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220281 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CC=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 71, 71, 71, 48, 48, 48, 10, 10, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 48, 48, 48, 48, 71, 71, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 3, 48] 71 rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 206 number of broken/clashed sets: 71 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220281 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CC=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 10, 10, 30, 30, 30, 30, 30, 48, 48, 30, 48, 48, 30, 1, 2, 2, 2, 3, 3, 10, 10, 30, 30, 30, 48, 48, 30, 48, 48, 30, 1] 71 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 42] set([4, 5, 6, 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, 39, 40, 41]) total number of confs: 165 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220281 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220281 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220281/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220281 Building REAL300000220282 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220282' /scratch/stefan/7769801/working/building/REAL300000220282 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220282 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220282/0 /scratch/stefan/7769801/working/building/REAL300000220282 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/283 `/scratch/stefan/7769801/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)O2)N1) `REAL300000220282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220282 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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: [68, 68, 68, 68, 95, 113, 113, 67, 68, 67, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 68, 68, 68, 68, 95, 95, 13, 13, 1, 1, 7, 7, 1, 7, 7, 68] 118 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 345 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220282 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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: [101, 101, 101, 101, 118, 118, 118, 101, 101, 101, 51, 51, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 101, 101, 101, 101, 118, 118, 51, 51, 7, 7, 1, 1, 1, 1, 1, 101] 118 rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 287 number of broken/clashed sets: 117 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220282 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 68, 68, 68, 68, 101, 101, 68, 101, 101, 68, 1, 2, 2, 2, 3, 3, 11, 11, 68, 68, 101, 101, 68, 101, 101, 1] 118 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 271 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220282 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220282 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220282/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220282 Building REAL300000220283 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220283' /scratch/stefan/7769801/working/building/REAL300000220283 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220283 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220283/0 /scratch/stefan/7769801/working/building/REAL300000220283 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/284 `/scratch/stefan/7769801/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC(Cl)=C2)=N1) `REAL300000220283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220283 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 17, 17, 17, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 17, 17, 13, 3, 3, 1, 1, 1] 17 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 43 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: REAL300000220283 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 13, 9, 13, 13, 13, 1, 2, 2, 2, 3, 3, 1, 9, 9, 13, 9, 13] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 62 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220283 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220283 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220283/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220283 Building REAL300000220284 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220284' /scratch/stefan/7769801/working/building/REAL300000220284 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220284 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220284/0 /scratch/stefan/7769801/working/building/REAL300000220284 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/285 `/scratch/stefan/7769801/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3CCCC3)=C2)=N1) `REAL300000220284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220284 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3CCCC3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 47, 57, 57, 25, 25, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 1, 25, 25, 25, 25, 47, 47, 25, 5, 5, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1] 201 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 245 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220284 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3CCCC3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 124, 201, 201, 201, 124, 124, 124, 48, 48, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 17, 124, 124, 124, 124, 201, 201, 124, 48, 48, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 676 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220284 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3CCCC3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 25, 25, 86, 124, 124, 124, 124, 25, 1, 2, 2, 2, 3, 3, 1, 9, 9, 25, 25, 25, 124, 124, 124, 124, 124, 124, 124, 124, 124, 25] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 294 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220284 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220284 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220284/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220284 Building REAL300000220285 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220285' /scratch/stefan/7769801/working/building/REAL300000220285 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220285 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220285/0 /scratch/stefan/7769801/working/building/REAL300000220285 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/286 `/scratch/stefan/7769801/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCN(C)CC3)C(F)=C2)=N1) `REAL300000220285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220285 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCN(C)CC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 15, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 41, 41, 41, 68, 88, 88, 41, 41, 41, 6, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 41, 42, 42, 42, 68, 68, 41, 6, 6, 1, 1, 9, 9, 9, 9, 10, 10, 10, 9, 9, 9, 9, 1] 118 rigid atoms, others: [36, 37, 49, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 314 number of broken/clashed sets: 118 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220285 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCN(C)CC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 15, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 95, 95, 95, 118, 118, 118, 95, 95, 95, 34, 34, 9, 2, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 94, 95, 95, 95, 118, 118, 95, 34, 34, 9, 9, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 9] 118 rigid atoms, others: [48, 38, 39, 40, 41, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 49]) total number of confs: 328 number of broken/clashed sets: 118 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220285 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCN(C)CC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 15, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 41, 41, 34, 41, 95, 95, 95, 95, 95, 95, 41, 41, 41, 1, 2, 2, 2, 3, 3, 1, 11, 11, 41, 41, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 41] 118 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220285 /scratch/stefan/7769801/working /scratch/stefan/7769801 mkdir: created directory `1' /scratch/stefan/7769801/working/building/REAL300000220285/1 /scratch/stefan/7769801/working/building/REAL300000220285 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/287 `/scratch/stefan/7769801/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CC[NH+](C)CC3)C(F)=C2)=N1) `REAL300000220285.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220285/1/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: REAL300000220285 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CC[NH+](C)CC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 9, 6, 5, 5, 5, 1, 15, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 36, 36, 36, 59, 83, 83, 36, 36, 36, 6, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 36, 36, 36, 36, 59, 59, 36, 6, 6, 1, 1, 8, 8, 8, 8, 8, 8, 7, 8, 8, 8, 8, 1] 100 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 50, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 290 number of broken/clashed sets: 100 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220285 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CC[NH+](C)CC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 9, 6, 5, 5, 5, 1, 15, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [73, 73, 73, 73, 100, 100, 100, 73, 73, 73, 24, 24, 7, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 73, 73, 73, 73, 100, 100, 73, 24, 24, 8, 8, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 8] 100 rigid atoms, others: [48, 49, 39, 40, 41, 42, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 50]) total number of confs: 295 number of broken/clashed sets: 100 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220285 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CC[NH+](C)CC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 9, 6, 5, 5, 5, 1, 15, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 36, 36, 36, 36, 73, 73, 73, 73, 73, 73, 73, 36, 36, 36, 1, 2, 2, 2, 3, 3, 1, 11, 11, 36, 36, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 36] 100 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220285 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220285 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 1: /scratch/stefan/7769801/working/building/REAL300000220285/1.* 0: /scratch/stefan/7769801/working/building/REAL300000220285/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220285 Building REAL300000220286 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220286' /scratch/stefan/7769801/working/building/REAL300000220286 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220286 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220286/0 /scratch/stefan/7769801/working/building/REAL300000220286 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/288 `/scratch/stefan/7769801/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3F)=C2)=N1) `REAL300000220286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220286 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 44, 73, 73, 23, 23, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 2, 9, 9, 9, 1, 23, 23, 23, 23, 44, 44, 23, 5, 5, 1, 1, 1, 2, 2, 9, 9, 8, 9, 1] 201 rigid atoms, others: [37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45]) total number of confs: 305 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220286 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 121, 121, 201, 201, 201, 121, 121, 121, 33, 33, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 121, 121, 121, 121, 201, 201, 121, 33, 33, 9, 8, 9, 6, 6, 1, 1, 1, 1, 9] 201 rigid atoms, others: [42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46]) total number of confs: 689 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220286 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 8, 8, 23, 23, 23, 23, 23, 39, 39, 121, 121, 53, 121, 121, 121, 23, 1, 2, 2, 2, 3, 3, 1, 8, 8, 23, 23, 23, 39, 39, 121, 121, 121, 121, 23] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 432 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220286 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220286 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220286/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220286 Building REAL300000220287 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220287' /scratch/stefan/7769801/working/building/REAL300000220287 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220287 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220287/0 /scratch/stefan/7769801/working/building/REAL300000220287 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/289 `/scratch/stefan/7769801/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)=CC1=CC=CC=C1) `REAL300000220287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220287 none CC(C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)=CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 9, 9, 24, 24, 24, 24, 24, 41, 41, 41, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 41, 41, 24, 24, 24, 24, 4, 1, 1, 1, 1, 1] 41 rigid atoms, others: [35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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: REAL300000220287 none CC(C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)=CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 23, 23, 24, 24, 23, 24, 24, 24, 24, 24, 10, 10, 3, 3, 2, 2, 2, 1, 24, 24, 24, 24, 24, 24] 41 rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220287 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220287 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220287/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220287 Building REAL300000220288 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220288' /scratch/stefan/7769801/working/building/REAL300000220288 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220288 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220288/0 /scratch/stefan/7769801/working/building/REAL300000220288 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/290 `/scratch/stefan/7769801/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CS2)C=C1) `REAL300000220288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220288 none CC1=CC=C(C2=NC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 14, 1, 1, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [2, 1, 3, 3, 1, 1, 1, 1, 1, 12, 12, 42, 42, 43, 43, 43, 63, 63, 63, 43, 43, 43, 1, 1, 3, 3, 4, 4, 4, 4, 4, 12, 12, 63, 63, 43, 43, 43, 43, 1, 4, 4] 63 rigid atoms, others: [4, 5, 6, 7, 8, 39, 22, 23] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220288 none CC1=CC=C(C2=NC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 14, 1, 1, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [52, 43, 52, 52, 43, 43, 43, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 43, 43, 52, 52, 52, 52, 52, 52, 52, 11, 11, 3, 3, 2, 2, 2, 1, 43, 52, 52] 63 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 150 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220288 none CC1=CC=C(C2=NC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 14, 1, 1, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [1, 1, 1, 1, 1, 1, 4, 4, 5, 30, 30, 53, 53, 53, 53, 53, 63, 63, 63, 53, 53, 53, 4, 4, 1, 1, 2, 2, 2, 1, 1, 30, 30, 63, 63, 53, 53, 53, 53, 4, 1, 1] 63 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 41, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220288 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220288 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220288/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220288 Building REAL300000220289 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220289' /scratch/stefan/7769801/working/building/REAL300000220289 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220289 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220289/0 /scratch/stefan/7769801/working/building/REAL300000220289 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/291 `/scratch/stefan/7769801/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC3=CC=CC=C3O2)N1) `REAL300000220289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220289 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC3=CC=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 97, 112, 112, 58, 58, 58, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 58, 59, 59, 59, 97, 97, 9, 9, 1, 2, 2, 2, 13, 13, 13, 13, 13, 58] 201 rigid atoms, others: [36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 393 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220289 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC3=CC=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 201, 201, 201, 155, 155, 155, 62, 62, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 201, 201, 62, 62, 13, 13, 13, 13, 1, 1, 1, 1, 1, 155] 201 rigid atoms, others: [40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45]) total number of confs: 544 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220289 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC3=CC=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 58, 58, 58, 58, 58, 58, 155, 155, 155, 155, 155, 155, 155, 155, 1, 2, 2, 2, 3, 3, 10, 10, 58, 59, 59, 59, 155, 155, 155, 155, 155, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 45, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 244 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220289 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220289 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220289/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220289 Building REAL300000220290 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220290' /scratch/stefan/7769801/working/building/REAL300000220290 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220290 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220290/0 /scratch/stefan/7769801/working/building/REAL300000220290 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/292 `/scratch/stefan/7769801/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=NC=C2)N1) `REAL300000220290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220290 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=NC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 126, 148, 148, 84, 84, 84, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 84, 84, 84, 84, 126, 126, 11, 11, 1, 2, 2, 2, 7, 7, 7, 7, 84] 156 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 468 number of broken/clashed sets: 155 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220290 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=NC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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: [140, 140, 140, 140, 156, 156, 156, 140, 140, 140, 43, 43, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 156, 156, 43, 43, 7, 7, 7, 7, 1, 1, 1, 1, 140] 156 rigid atoms, others: [37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 317 number of broken/clashed sets: 155 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220290 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=NC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 84, 84, 84, 84, 84, 84, 140, 140, 84, 140, 140, 1, 2, 2, 2, 3, 3, 11, 11, 84, 84, 84, 84, 140, 140, 140, 140, 1] 156 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 41, 25] set([4, 5, 6, 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, 39, 40]) total number of confs: 357 number of broken/clashed sets: 155 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220290 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220290 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220290/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220290 Building REAL300000220291 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220291' /scratch/stefan/7769801/working/building/REAL300000220291 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220291 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220291/0 /scratch/stefan/7769801/working/building/REAL300000220291 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/293 `/scratch/stefan/7769801/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C([N+](=O)[O-])C=C2)N1) `REAL300000220291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220291 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C([N+](=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 123, 131, 131, 73, 73, 73, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 7, 7, 73, 73, 73, 73, 123, 123, 12, 12, 1, 2, 2, 2, 7, 7, 7, 7, 73] 163 rigid atoms, others: [36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 455 number of broken/clashed sets: 162 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220291 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C([N+](=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 163, 163, 163, 114, 114, 114, 41, 41, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 114, 114, 114, 114, 163, 163, 41, 41, 7, 7, 7, 7, 1, 1, 1, 1, 114] 163 rigid atoms, others: [40, 41, 42, 43, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44]) total number of confs: 490 number of broken/clashed sets: 162 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220291 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C([N+](=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 73, 73, 73, 73, 73, 73, 114, 114, 106, 114, 114, 114, 114, 114, 1, 2, 2, 2, 3, 3, 11, 11, 73, 73, 73, 73, 114, 114, 114, 114, 1] 163 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 44, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 234 number of broken/clashed sets: 162 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220291 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220291 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220291/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220291 Building REAL300000220292 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220292' /scratch/stefan/7769801/working/building/REAL300000220292 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220292 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220292/0 /scratch/stefan/7769801/working/building/REAL300000220292 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/294 `/scratch/stefan/7769801/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(C)(=O)=O)C=C2)=N1) `REAL300000220292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220292 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(C)(=O)=O)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 21, 21, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 11, 11, 11, 11, 17, 17, 11, 4, 4, 1, 1, 3, 3, 3, 1, 1] 31 rigid atoms, others: [32, 33, 37, 38, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 80 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: REAL300000220292 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(C)(=O)=O)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 7, 7, 11, 11, 7, 7, 21, 21, 21, 11, 11, 1, 2, 2, 2, 3, 3, 1, 7, 7, 11, 11, 21, 21, 21, 11, 11] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 118 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220292 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220292 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220292/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220292 Building REAL300000220293 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220293' /scratch/stefan/7769801/working/building/REAL300000220293 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220293 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220293/0 /scratch/stefan/7769801/working/building/REAL300000220293 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/295 `/scratch/stefan/7769801/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=C2COC3=CC=C(F)C=C23)N1) `REAL300000220293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220293 none CC1=C(CC(=O)[O-])C(=O)N=C(C=C2COC3=CC=C(F)C=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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, 9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 1, 1, 1, 1, 1, 1, 5] 9 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 22, 23, 24, 25, 26, 27]) total number of confs: 30 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: REAL300000220293 none CC1=C(CC(=O)[O-])C(=O)N=C(C=C2COC3=CC=C(F)C=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 3, 3, 5, 5, 5, 5, 5, 5, 1] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 26 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220293 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220293 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220293/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220293 Building REAL300000220294 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220294' /scratch/stefan/7769801/working/building/REAL300000220294 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220294 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220294/0 /scratch/stefan/7769801/working/building/REAL300000220294 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/296 `/scratch/stefan/7769801/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C(C)(C)C)N1) `REAL300000220294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220294 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C(C)(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 35, 35, 35, 48, 48, 48, 35, 35, 35, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 35, 36, 36, 36, 48, 48, 7, 7, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35] 52 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 157 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220294 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C(C)(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 35, 35, 35, 35, 35, 38, 38, 38, 1, 2, 2, 2, 3, 3, 12, 12, 35, 35, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1] 52 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 41] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 122 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220294 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220294 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220294/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220294 Building REAL300000220295 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220295' /scratch/stefan/7769801/working/building/REAL300000220295 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220295 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220295/0 /scratch/stefan/7769801/working/building/REAL300000220295 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/297 `/scratch/stefan/7769801/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2[N+](=O)[O-])OCCO3)=N1) `REAL300000220295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220295 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2[N+](=O)[O-])OCCO3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 5, 5, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 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: [31, 31, 31, 31, 37, 37, 37, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 31, 31, 31, 31, 37, 37, 31, 7, 7, 1, 1, 1, 1, 1, 1] 37 rigid atoms, others: [35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 83 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: REAL300000220295 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2[N+](=O)[O-])OCCO3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 5, 5, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 1, 11, 11, 31, 31, 31, 31, 31, 31] 37 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 77 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220295 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220295 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220295/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220295 Building REAL300000220296 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220296' /scratch/stefan/7769801/working/building/REAL300000220296 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220296 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220296/0 /scratch/stefan/7769801/working/building/REAL300000220296 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/298 `/scratch/stefan/7769801/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=CC=C3OCOC3=C2)N1) `REAL300000220296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220296 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=CC=C3OCOC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 100, 120, 120, 60, 61, 60, 12, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 10, 11, 11, 11, 11, 11, 61, 61, 61, 61, 100, 100, 12, 12, 1, 1, 11, 11, 11, 11, 11, 61] 201 rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 416 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220296 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=CC=C3OCOC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 141, 201, 201, 201, 141, 141, 141, 56, 56, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 201, 201, 56, 56, 11, 11, 1, 1, 1, 1, 1, 141] 201 rigid atoms, others: [37, 38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 604 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220296 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=CC=C3OCOC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 61, 61, 61, 61, 61, 141, 141, 141, 141, 141, 141, 141, 141, 1, 2, 2, 2, 3, 3, 10, 10, 61, 61, 141, 141, 141, 141, 141, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 27, 42] set([4, 5, 6, 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, 41]) total number of confs: 226 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220296 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220296 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220296/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220296 Building REAL300000220297 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220297' /scratch/stefan/7769801/working/building/REAL300000220297 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220297 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220297/0 /scratch/stefan/7769801/working/building/REAL300000220297 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/299 `/scratch/stefan/7769801/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OC2CCCC2)=N1) `REAL300000220297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220297 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OC2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 93, 127, 127, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 50, 50, 50, 50, 93, 93, 50, 8, 8, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 486 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220297 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OC2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 115, 201, 201, 201, 115, 115, 115, 37, 37, 12, 12, 12, 9, 12, 12, 6, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 201, 201, 115, 37, 37, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 724 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220297 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OC2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 50, 50, 31, 50, 50, 50, 101, 115, 115, 115, 115, 1, 2, 2, 2, 3, 3, 1, 11, 11, 50, 50, 50, 50, 115, 115, 115, 115, 115, 115, 115, 115, 115] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 306 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220297 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220297 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220297/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220297 Building REAL300000220298 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220298' /scratch/stefan/7769801/working/building/REAL300000220298 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220298 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220298/0 /scratch/stefan/7769801/working/building/REAL300000220298 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/300 `/scratch/stefan/7769801/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CSC=C3)=N2)=N1) `REAL300000220298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220298 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CSC=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 14, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 52, 52, 52, 74, 75, 75, 52, 52, 52, 12, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 52, 53, 53, 53, 74, 74, 51, 13, 12, 1, 5, 5, 5] 110 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 224 number of broken/clashed sets: 109 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220298 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CSC=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 14, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [92, 92, 92, 92, 110, 110, 110, 92, 92, 92, 31, 31, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 92, 92, 92, 92, 110, 110, 91, 31, 31, 5, 1, 1, 1] 110 rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 255 number of broken/clashed sets: 109 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220298 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CSC=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 14, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 52, 52, 52, 52, 92, 92, 92, 92, 52, 1, 2, 2, 2, 3, 3, 1, 12, 12, 52, 92, 92, 92] 110 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 173 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220298 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220298 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220298/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220298 Building REAL300000220299 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220299' /scratch/stefan/7769801/working/building/REAL300000220299 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220299 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220299/0 /scratch/stefan/7769801/working/building/REAL300000220299 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/301 `/scratch/stefan/7769801/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC([N+](=O)[O-])=CC=C2OC(F)F)=N1) `REAL300000220299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220299 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC([N+](=O)[O-])=CC=C2OC(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 85, 143, 143, 56, 56, 56, 9, 9, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 40, 40, 56, 56, 56, 56, 85, 85, 56, 9, 9, 1, 1, 1, 40] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 606 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220299 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC([N+](=O)[O-])=CC=C2OC(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 56, 56, 56, 56, 56, 23, 56, 56, 56, 130, 182, 182, 1, 2, 2, 2, 3, 3, 1, 11, 11, 56, 56, 56, 182] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 635 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220299 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220299 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220299/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220299 Building REAL300000220300 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220300' /scratch/stefan/7769801/working/building/REAL300000220300 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220300 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220300/0 /scratch/stefan/7769801/working/building/REAL300000220300 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/302 `/scratch/stefan/7769801/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)S2)C=C1) `REAL300000220300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220300 none CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 7, 7, 1, 1, 1, 1, 1, 1, 11, 11, 45, 45, 45, 45, 45, 55, 56, 56, 45, 45, 45, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 11, 11, 55, 55, 45, 45, 45, 45, 7, 7] 91 rigid atoms, others: [4, 5, 6, 7, 8, 9, 32, 23, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220300 none CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [76, 76, 79, 79, 45, 45, 45, 45, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 45, 79, 79, 79, 79, 79, 79, 79, 45, 45, 11, 11, 3, 3, 2, 2, 2, 1, 79, 79] 91 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 181 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220300 none CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 1, 7, 7, 7, 7, 41, 41, 79, 79, 79, 79, 79, 91, 91, 91, 79, 79, 79, 7, 1, 1, 2, 2, 2, 1, 1, 7, 7, 41, 41, 91, 91, 79, 79, 79, 79, 1, 1] 91 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 42, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220300 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220300 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220300/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220300 Building REAL300000220301 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220301' /scratch/stefan/7769801/working/building/REAL300000220301 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220301 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220301/0 /scratch/stefan/7769801/working/building/REAL300000220301 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/303 `/scratch/stefan/7769801/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1) `REAL300000220301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220301 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 67, 104, 67, 67, 67, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 67, 104, 104, 104, 68, 68, 12, 12, 2, 2, 2, 3, 3, 1] 124 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 261 number of broken/clashed sets: 123 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220301 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 67, 67, 97, 101, 101, 67, 68, 67, 1, 13, 13, 13, 1, 1, 12, 12, 68, 68, 68, 97, 97, 67] 124 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 318 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220301 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220301 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220301/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220301 Building REAL300000220302 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220302' /scratch/stefan/7769801/working/building/REAL300000220302 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220302 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220302/0 /scratch/stefan/7769801/working/building/REAL300000220302 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/304 `/scratch/stefan/7769801/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CO2)=N1) `REAL300000220302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220302 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CO2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 33, 33, 33, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 33, 33, 27, 10, 9, 1, 1] 33 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 82 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: REAL300000220302 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CO2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 1, 9, 9, 27, 27] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 66 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220302 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220302 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220302/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220302 Building REAL300000220303 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220303' /scratch/stefan/7769801/working/building/REAL300000220303 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220303 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220303/0 /scratch/stefan/7769801/working/building/REAL300000220303 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/305 `/scratch/stefan/7769801/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN3C=C(Cl)C=CC3=N2)N1) `REAL300000220303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220303 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN3C=C(Cl)C=CC3=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 16, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 19, 19, 19, 29, 29, 29, 18, 19, 18, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 29, 29, 11, 11, 1, 1, 1, 1, 19] 29 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 100 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: REAL300000220303 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN3C=C(Cl)C=CC3=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 16, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 11, 11, 19, 19, 19, 19, 1] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 59 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220303 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220303 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220303/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220303 Building REAL300000220304 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220304' /scratch/stefan/7769801/working/building/REAL300000220304 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220304 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220304/0 /scratch/stefan/7769801/working/building/REAL300000220304 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/306 `/scratch/stefan/7769801/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C3OC(C)(C)CCC3=C2)=N1) `REAL300000220304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220304 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C3OC(C)(C)CCC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 32, 32, 32, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 32, 32, 18, 6, 6, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1] 32 rigid atoms, others: [34, 35, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 127 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: REAL300000220304 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C3OC(C)(C)CCC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 3, 1, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 59 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220304 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220304 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220304/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220304 Building REAL300000220305 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220305' /scratch/stefan/7769801/working/building/REAL300000220305 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220305 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220305/0 /scratch/stefan/7769801/working/building/REAL300000220305 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/307 `/scratch/stefan/7769801/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(C)C(=O)[O-])=C2)=N1) `REAL300000220305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220305 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(C)C(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 50, 83, 83, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 23, 23, 1, 29, 29, 29, 29, 50, 50, 29, 5, 5, 1, 1, 1, 15, 15, 15, 15, 1] 201 rigid atoms, others: [34, 35, 36, 41, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 368 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220305 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(C)C(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 29, 29, 76, 128, 128, 167, 167, 29, 1, 2, 2, 2, 3, 3, 1, 9, 9, 29, 29, 29, 128, 128, 128, 128, 29] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 552 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220305 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220305 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220305/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220305 Building REAL300000220306 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220306' /scratch/stefan/7769801/working/building/REAL300000220306 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220306 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220306/0 /scratch/stefan/7769801/working/building/REAL300000220306 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/308 `/scratch/stefan/7769801/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCCCC#N) `REAL300000220306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220306 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCCCC#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 55, 60, 107, 123, 123, 38, 38, 38, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 60, 60, 107, 107, 123, 123] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 542 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220306 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCCCC#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 35, 54, 54, 21, 21, 21, 1, 1, 1, 5, 9, 15, 17, 17, 3, 3, 3, 1, 1, 5, 5, 21, 21, 21, 35, 35, 21, 1, 9, 9, 15, 15, 17, 17] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 41, 20, 21, 22, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 259 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220306 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220306 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220306/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220306 Building REAL300000220307 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220307' /scratch/stefan/7769801/working/building/REAL300000220307 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220307 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220307/0 /scratch/stefan/7769801/working/building/REAL300000220307 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/309 `/scratch/stefan/7769801/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(F)(F)F)C=C2)=N1) `REAL300000220307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220307 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 42, 64, 64, 26, 26, 26, 4, 4, 1, 1, 1, 1, 1, 1, 7, 26, 26, 26, 26, 1, 1, 26, 26, 26, 26, 42, 42, 26, 4, 4, 1, 1, 26, 26, 1, 1] 201 rigid atoms, others: [34, 35, 38, 39, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 288 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220307 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 13, 13, 26, 26, 13, 13, 71, 145, 145, 145, 145, 26, 26, 1, 2, 2, 2, 3, 3, 1, 13, 13, 26, 26, 145, 145, 26, 26] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 516 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220307 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220307 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220307/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220307 Building REAL300000220308 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220308' /scratch/stefan/7769801/working/building/REAL300000220308 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220308 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220308/0 /scratch/stefan/7769801/working/building/REAL300000220308 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/310 `/scratch/stefan/7769801/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC) `REAL300000220308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220308 none CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 64, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 62, 97, 145, 145, 145, 145, 145, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 97, 97, 97, 97, 97] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 40, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 730 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220308 none CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 5, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 40, 64, 64, 21, 21, 21, 1, 1, 1, 7, 15, 22, 22, 22, 22, 22, 1, 1, 5, 5, 21, 21, 21, 40, 40, 21, 1, 15, 15, 16, 16, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 41, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 358 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220308 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220308 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220308/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220308 Building REAL300000220309 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220309' /scratch/stefan/7769801/working/building/REAL300000220309 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220309 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220309/0 /scratch/stefan/7769801/working/building/REAL300000220309 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/311 `/scratch/stefan/7769801/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)COC1=C(C)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C) `REAL300000220309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220309 none COC(=O)COC1=C(C)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 88, 151, 29, 26, 19, 29, 29, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 29, 29, 29, 151, 151, 151, 88, 88, 29, 29, 29, 29, 10, 10, 2, 2, 2, 3, 3, 1, 29, 29, 29, 29] 201 rigid atoms, others: [44, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 598 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220309 none COC(=O)COC1=C(C)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 5, 26, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 57, 97, 97, 29, 29, 29, 1, 1, 1, 27, 27, 27, 5, 5, 2, 2, 2, 1, 5, 5, 29, 29, 29, 57, 57, 29, 1, 2, 2, 2] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 45, 25, 36, 26, 27] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 442 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220309 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220309 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220309/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220309 Building REAL300000220310 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220310' /scratch/stefan/7769801/working/building/REAL300000220310 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220310 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220310/0 /scratch/stefan/7769801/working/building/REAL300000220310 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/312 `/scratch/stefan/7769801/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220310 none COCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 113, 63, 63, 21, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 140, 140, 140, 140, 140, 113, 113, 63, 63, 21, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21] 201 rigid atoms, others: [45, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46]) total number of confs: 484 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220310 none COCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 40, 48, 48, 21, 21, 21, 1, 15, 15, 15, 14, 14, 10, 10, 6, 6, 1, 1, 1, 5, 5, 21, 21, 21, 40, 40, 21, 1] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 46, 25, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220310 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220310 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220310/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220310 Building REAL300000220311 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220311' /scratch/stefan/7769801/working/building/REAL300000220311 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220311 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220311/0 /scratch/stefan/7769801/working/building/REAL300000220311 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/313 `/scratch/stefan/7769801/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1SC) `REAL300000220311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220311 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'S.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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 46, 46, 46, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 46, 46, 46, 46, 154, 95, 95, 95, 46, 12, 12, 3, 3, 2, 2, 2, 1, 46, 46, 154, 154, 154] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 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: 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: REAL300000220311 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'S.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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 46, 46, 46, 46, 46, 77, 127, 127, 46, 46, 46, 1, 1, 1, 1, 9, 4, 4, 4, 1, 6, 6, 77, 77, 46, 46, 46, 46, 1, 1, 10, 10, 10] 201 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 36, 27, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 459 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220311 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220311 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220311/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220311 Building REAL300000220312 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220312' /scratch/stefan/7769801/working/building/REAL300000220312 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220312 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220312/0 /scratch/stefan/7769801/working/building/REAL300000220312 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/314 `/scratch/stefan/7769801/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC(C)C)=C2)N1) `REAL300000220312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220312 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC(C)C)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 67, 100, 100, 36, 36, 36, 5, 5, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 1, 36, 36, 36, 36, 67, 67, 5, 5, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 1, 36] 201 rigid atoms, others: [32, 33, 41, 12, 13, 14, 15, 16, 17, 18, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 421 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220312 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC(C)C)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 36, 36, 36, 36, 36, 123, 148, 148, 36, 1, 2, 2, 2, 3, 3, 10, 10, 36, 36, 36, 148, 148, 148, 148, 148, 148, 148, 36, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 42] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 345 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220312 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220312 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220312/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220312 Building REAL300000220313 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220313' /scratch/stefan/7769801/working/building/REAL300000220313 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220313 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220313/0 /scratch/stefan/7769801/working/building/REAL300000220313 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/315 `/scratch/stefan/7769801/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCCC(=O)[O-])=C2)=N1) `REAL300000220313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220313 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCCC(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 55, 87, 87, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 7, 9, 15, 15, 1, 29, 29, 29, 29, 55, 55, 29, 5, 5, 1, 1, 1, 7, 7, 9, 9, 1] 201 rigid atoms, others: [34, 35, 36, 41, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 374 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220313 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCCC(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 29, 29, 120, 122, 128, 156, 156, 29, 1, 2, 2, 2, 3, 3, 1, 9, 9, 29, 29, 29, 122, 122, 128, 128, 29] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 351 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220313 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220313 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220313/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220313 Building REAL300000220314 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220314' /scratch/stefan/7769801/working/building/REAL300000220314 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220314 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220314/0 /scratch/stefan/7769801/working/building/REAL300000220314 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/316 `/scratch/stefan/7769801/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC(F)=CC(F)=C3)C=C2)=N1) `REAL300000220314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220314 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC(F)=CC(F)=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 30, 45, 45, 19, 19, 19, 4, 4, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 11, 19, 19, 19, 1, 1, 19, 19, 19, 19, 30, 30, 19, 4, 4, 1, 1, 19, 11, 19, 1, 1] 201 rigid atoms, others: [37, 38, 42, 43, 12, 13, 14, 15, 16, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 193 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220314 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC(F)=CC(F)=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 153, 201, 201, 201, 153, 153, 153, 51, 51, 8, 8, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 153, 153, 153, 153, 201, 201, 153, 51, 51, 26, 26, 1, 1, 1, 26, 26] 201 rigid atoms, others: [39, 40, 41, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43]) total number of confs: 592 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220314 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC(F)=CC(F)=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 19, 19, 12, 18, 86, 139, 139, 139, 102, 139, 139, 139, 19, 19, 1, 2, 2, 2, 3, 3, 1, 12, 12, 19, 19, 139, 103, 139, 19, 19] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 354 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220314 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220314 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220314/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220314 Building REAL300000220315 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220315' /scratch/stefan/7769801/working/building/REAL300000220315 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220315 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220315/0 /scratch/stefan/7769801/working/building/REAL300000220315 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/317 `/scratch/stefan/7769801/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(F)=C2)=N1) `REAL300000220315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220315 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 20, 20, 20, 29, 29, 29, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 29, 29, 20, 7, 7, 1, 1, 1] 29 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 87 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220315 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 1, 9, 9, 20, 20, 20] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 61 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220315 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220315 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220315/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220315 Building REAL300000220316 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220316' /scratch/stefan/7769801/working/building/REAL300000220316 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220316 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220316/0 /scratch/stefan/7769801/working/building/REAL300000220316 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/318 `/scratch/stefan/7769801/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Cl)C=C(Cl)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220316 none COC1=C(Cl)C=C(Cl)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [70, 60, 60, 60, 60, 28, 60, 60, 60, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 70, 70, 70, 60, 60, 12, 12, 2, 2, 2, 3, 3, 1] 96 rigid atoms, others: [36, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 235 number of broken/clashed sets: 96 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220316 none COC1=C(Cl)C=C(Cl)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 60, 60, 60, 60, 60, 87, 96, 96, 60, 60, 60, 7, 7, 7, 1, 1, 11, 11, 60, 60, 60, 87, 87, 60] 96 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 287 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220316 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220316 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220316/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220316 Building REAL300000220317 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220317' /scratch/stefan/7769801/working/building/REAL300000220317 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220317 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220317/0 /scratch/stefan/7769801/working/building/REAL300000220317 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/319 `/scratch/stefan/7769801/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC) `REAL300000220317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220317 none CCOCC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 100, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 27, 27, 19, 26, 65, 125, 125, 125, 125, 125, 100, 100, 27, 9, 9, 2, 2, 2, 3, 3, 1, 27, 27, 65, 65, 65] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 508 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220317 none CCOCC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 5, 1, 1, 1, 1, 1, 5, 5, 27, 27, 27, 27, 27, 46, 69, 69, 27, 27, 27, 1, 1, 1, 1, 3, 11, 11, 11, 10, 10, 5, 5, 1, 5, 5, 27, 27, 27, 46, 46, 27, 1, 1, 4, 4, 4] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 42, 43, 21, 22, 23, 24] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 278 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220317 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220317 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220317/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220317 Building REAL300000220318 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220318' /scratch/stefan/7769801/working/building/REAL300000220318 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220318 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220318/0 /scratch/stefan/7769801/working/building/REAL300000220318 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/320 `/scratch/stefan/7769801/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([N+](=O)[O-])C([O-])=C2)N1) `REAL300000220318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220318 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([N+](=O)[O-])C([O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 4, 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: [25, 25, 25, 25, 28, 28, 28, 25, 25, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 28, 28, 7, 7, 1, 1, 1, 25] 28 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 56 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: REAL300000220318 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([N+](=O)[O-])C([O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 10, 10, 25, 25, 25, 1] 28 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 71 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220318 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220318 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220318/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220318 Building REAL300000220319 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220319' /scratch/stefan/7769801/working/building/REAL300000220319 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220319 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220319/0 /scratch/stefan/7769801/working/building/REAL300000220319 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/321 `/scratch/stefan/7769801/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=NC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C12) `REAL300000220319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220319 none CC1=NN(C)C2=NC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 3, 3, 2, 2, 2, 1, 16] 29 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) 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: REAL300000220319 none CC1=NN(C)C2=NC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 16, 29, 29, 29, 16, 16, 16, 1, 1, 2, 2, 2, 2, 2, 2, 1, 5, 5, 29, 29, 16, 16, 16, 16, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 40, 23, 24, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220319 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220319 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220319/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220319 Building REAL300000220320 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220320' /scratch/stefan/7769801/working/building/REAL300000220320 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220320 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220320/0 /scratch/stefan/7769801/working/building/REAL300000220320 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/322 `/scratch/stefan/7769801/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)C2=CC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CN=C2S1) `REAL300000220320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220320 none COC(=O)C1=C(C)C2=CC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CN=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 41, 101, 41, 41, 41, 41, 41, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 41, 41, 41, 41, 101, 101, 101, 41, 41, 41, 41, 12, 12, 2, 2, 2, 3, 3, 1, 41] 131 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43]) total number of confs: 277 number of broken/clashed sets: 131 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220320 none COC(=O)C1=C(C)C2=CC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CN=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 41, 41, 72, 94, 94, 41, 41, 41, 1, 1, 1, 1, 13, 13, 13, 2, 2, 2, 1, 7, 7, 41, 41, 41, 72, 72, 41, 1] 131 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 43, 34, 24, 25, 26, 27] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 361 number of broken/clashed sets: 131 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220320 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220320 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220320/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220320 Building REAL300000220321 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220321' /scratch/stefan/7769801/working/building/REAL300000220321 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220321 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220321/0 /scratch/stefan/7769801/working/building/REAL300000220321 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/323 `/scratch/stefan/7769801/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC) `REAL300000220321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220321 none C=C(C)COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 121, 137, 96, 27, 27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 27, 27, 27, 27, 51, 137, 137, 137, 137, 137, 121, 121, 27, 8, 8, 2, 2, 2, 3, 3, 1, 27, 27, 51, 51, 51] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 422 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220321 none C=C(C)COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 20, 25, 7, 1, 1, 1, 1, 1, 5, 5, 27, 27, 27, 27, 27, 49, 82, 82, 27, 27, 27, 1, 1, 1, 1, 3, 25, 25, 25, 25, 25, 20, 20, 1, 5, 5, 27, 27, 27, 49, 49, 27, 1, 1, 3, 3, 3] 201 rigid atoms, others: [34, 4, 5, 6, 7, 8, 43, 44, 22, 23, 24, 25] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 388 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220321 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220321 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220321/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220321 Building REAL300000220322 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220322' /scratch/stefan/7769801/working/building/REAL300000220322 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220322 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220322/0 /scratch/stefan/7769801/working/building/REAL300000220322 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/324 `/scratch/stefan/7769801/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220322 none CCCCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 60, 60, 21, 21, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 60, 60, 21, 21, 21, 6, 6, 2, 2, 2, 3, 3, 1, 21] 201 rigid atoms, others: [50, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51]) total number of confs: 440 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220322 none CCCCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 34, 44, 44, 21, 21, 21, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 1, 1, 1, 5, 5, 21, 21, 21, 34, 34, 21, 1] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 40, 51, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 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, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 191 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220322 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220322 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220322/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220322 Building REAL300000220323 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220323' /scratch/stefan/7769801/working/building/REAL300000220323 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220323 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220323/0 /scratch/stefan/7769801/working/building/REAL300000220323 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/325 `/scratch/stefan/7769801/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1O) `REAL300000220323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220323 none C=CCC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 3, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [97, 63, 29, 29, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 29, 29, 29, 62, 29, 29, 97, 97, 97, 63, 63, 29, 10, 10, 3, 3, 1, 1, 1, 1, 29, 62, 62, 62, 58] 402 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 471 number of broken/clashed sets: 203 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220323 none C=CCC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 3, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 54, 93, 93, 29, 29, 29, 1, 1, 1, 3, 1, 1, 11, 11, 11, 5, 5, 1, 5, 5, 54, 54, 29, 29, 29, 29, 1, 3, 3, 3, 2] 402 rigid atoms, others: [2, 3, 4, 5, 6, 40, 20, 21, 22, 24, 25, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 379 number of broken/clashed sets: 203 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220323 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220323 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220323/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220323 Building REAL300000220324 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220324' /scratch/stefan/7769801/working/building/REAL300000220324 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220324 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220324/0 /scratch/stefan/7769801/working/building/REAL300000220324 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/326 `/scratch/stefan/7769801/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(F)F)=C2)=N1) `REAL300000220324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220324 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 51, 68, 68, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 10, 16, 16, 1, 29, 29, 29, 29, 51, 51, 29, 5, 5, 1, 1, 1, 16, 1] 201 rigid atoms, others: [32, 33, 34, 36, 12, 13, 14, 15, 16, 17, 18, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 279 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220324 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 29, 29, 98, 128, 128, 29, 1, 2, 2, 2, 3, 3, 1, 9, 9, 29, 29, 29, 128, 29] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 346 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220324 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220324 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220324/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220324 Building REAL300000220325 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220325' /scratch/stefan/7769801/working/building/REAL300000220325 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220325 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220325/0 /scratch/stefan/7769801/working/building/REAL300000220325 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/327 `/scratch/stefan/7769801/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC) `REAL300000220325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220325 none CCCCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 90, 85, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 19, 19, 19, 19, 34, 139, 139, 139, 139, 139, 139, 139, 139, 139, 90, 90, 19, 5, 5, 2, 2, 2, 3, 3, 1, 19, 19, 34, 34, 34] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52]) total number of confs: 447 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220325 none CCCCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 9, 7, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 19, 32, 35, 35, 19, 19, 19, 1, 1, 1, 1, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 1, 5, 5, 19, 19, 19, 32, 32, 19, 1, 1, 3, 3, 3] 201 rigid atoms, others: [5, 6, 39, 8, 9, 7, 48, 49, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220325 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220325 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220325/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220325 Building REAL300000220326 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220326' /scratch/stefan/7769801/working/building/REAL300000220326 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220326 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220326/0 /scratch/stefan/7769801/working/building/REAL300000220326 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/328 `/scratch/stefan/7769801/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3OC2)N1) `REAL300000220326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220326 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3OC2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 25, 25, 3, 3, 1, 1, 1, 1, 1, 1, 1, 13] 25 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 95 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: REAL300000220326 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3OC2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 3, 3, 5, 5, 13, 13, 13, 13, 13, 13, 13, 1] 25 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 47 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220326 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220326 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220326/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220326 Building REAL300000220327 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220327' /scratch/stefan/7769801/working/building/REAL300000220327 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220327 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220327/0 /scratch/stefan/7769801/working/building/REAL300000220327 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/329 `/scratch/stefan/7769801/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=CC(Cl)=CC(Cl)=C3OC2)=N1) `REAL300000220327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220327 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=CC(Cl)=CC(Cl)=C3OC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 29, 29, 29, 21, 21, 21, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 29, 29, 21, 3, 3, 1, 1, 1, 1, 1] 29 rigid atoms, others: [34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 32, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 76 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220327 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=CC(Cl)=CC(Cl)=C3OC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 10, 10, 21, 21, 21, 21, 21] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220327 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220327 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220327/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220327 Building REAL300000220328 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220328' /scratch/stefan/7769801/working/building/REAL300000220328 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220328 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220328/0 /scratch/stefan/7769801/working/building/REAL300000220328 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/330 `/scratch/stefan/7769801/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(Br)C=C1O) `REAL300000220328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220328 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(Br)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 4, 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: [65, 41, 41, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 41, 41, 41, 41, 41, 65, 65, 65, 41, 11, 11, 2, 2, 2, 3, 3, 1, 41, 82] 162 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 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: 162 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220328 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(Br)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 9, 9, 41, 41, 41, 41, 41, 63, 81, 81, 41, 41, 41, 1, 1, 1, 1, 1, 4, 4, 4, 1, 9, 9, 41, 41, 41, 63, 63, 41, 1, 2] 162 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 36, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 274 number of broken/clashed sets: 162 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220328 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220328 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220328/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220328 Building REAL300000220329 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220329' /scratch/stefan/7769801/working/building/REAL300000220329 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220329 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220329/0 /scratch/stefan/7769801/working/building/REAL300000220329 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/331 `/scratch/stefan/7769801/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C(Cl)=C2)N1) `REAL300000220329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220329 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 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: [22, 22, 22, 22, 27, 27, 27, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 27, 27, 6, 6, 1, 1, 2, 1, 22] 54 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 31, 33]) total number of confs: 66 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220329 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 22, 22, 20, 20, 22, 22, 22, 1, 2, 2, 2, 3, 3, 9, 9, 22, 22, 44, 22, 1] 54 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 114 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220329 /scratch/stefan/7769801/working /scratch/stefan/7769801 mkdir: created directory `1' /scratch/stefan/7769801/working/building/REAL300000220329/1 /scratch/stefan/7769801/working/building/REAL300000220329 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 1 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/332 `/scratch/stefan/7769801/working/3D/332' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([O-])C(Cl)=C2)N1) `REAL300000220329.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220329/1/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: REAL300000220329 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([O-])C(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 19, 19, 19, 29, 29, 29, 19, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 29, 29, 7, 7, 1, 1, 1, 19] 29 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 92 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220329 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([O-])C(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 19, 19, 15, 17, 19, 19, 19, 1, 2, 2, 2, 3, 3, 9, 9, 19, 19, 19, 1] 29 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 76 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220329 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220329 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 1: /scratch/stefan/7769801/working/building/REAL300000220329/1.* 0: /scratch/stefan/7769801/working/building/REAL300000220329/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220329 Building REAL300000220330 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220330' /scratch/stefan/7769801/working/building/REAL300000220330 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220330 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220330/0 /scratch/stefan/7769801/working/building/REAL300000220330 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/333 `/scratch/stefan/7769801/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220330 none CCCCCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 131, 131, 131, 131, 60, 60, 20, 20, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 20, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 60, 60, 20, 20, 20, 6, 6, 2, 2, 2, 3, 3, 1, 20] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 53, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54]) total number of confs: 452 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220330 none CCCCCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 20, 20, 20, 20, 20, 33, 42, 42, 20, 20, 20, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 1, 1, 1, 5, 5, 20, 20, 20, 33, 33, 20, 1] 201 rigid atoms, others: [11, 7, 8, 9, 10, 43, 44, 45, 12, 13, 54, 27] set([0, 1, 2, 3, 4, 5, 6, 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, 41, 42, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220330 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220330 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220330/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220330 Building REAL300000220331 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220331' /scratch/stefan/7769801/working/building/REAL300000220331 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220331 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220331/0 /scratch/stefan/7769801/working/building/REAL300000220331 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/334 `/scratch/stefan/7769801/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCCC(C)C) `REAL300000220331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220331 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 20, 20, 20, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 20, 20, 20, 67, 71, 120, 120, 120, 38, 38, 38, 20, 20, 5, 5, 2, 2, 2, 3, 3, 1, 20, 71, 71, 120, 120, 120, 120, 120, 120, 120, 120, 120] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 474 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220331 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 20, 20, 20, 20, 20, 37, 57, 57, 20, 20, 20, 1, 1, 1, 5, 7, 12, 12, 12, 3, 3, 3, 1, 1, 5, 5, 20, 20, 20, 37, 37, 20, 1, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 41, 20, 21, 22, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 262 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220331 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220331 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220331/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220331 Building REAL300000220332 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220332' /scratch/stefan/7769801/working/building/REAL300000220332 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220332 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220332/0 /scratch/stefan/7769801/working/building/REAL300000220332 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/335 `/scratch/stefan/7769801/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(F)(F)F) `REAL300000220332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220332 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 29, 29, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 29, 29, 29, 29, 101, 141, 141, 141, 141, 67, 67, 67, 29, 9, 9, 2, 2, 2, 3, 3, 1, 29, 29, 141, 141] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 39] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 459 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220332 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 50, 82, 82, 29, 29, 29, 1, 1, 1, 1, 7, 18, 18, 18, 18, 3, 3, 3, 1, 5, 5, 29, 29, 29, 50, 50, 29, 1, 1, 18, 18] 201 rigid atoms, others: [1, 2, 3, 4, 5, 40, 41, 19, 20, 21, 22, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43]) total number of confs: 354 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220332 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220332 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220332/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220332 Building REAL300000220333 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220333' /scratch/stefan/7769801/working/building/REAL300000220333 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220333 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220333/0 /scratch/stefan/7769801/working/building/REAL300000220333 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/336 `/scratch/stefan/7769801/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC(F)=C3)S2)N1) `REAL300000220333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220333 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC(F)=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 64, 64, 97, 110, 110, 64, 64, 64, 11, 11, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 1, 65, 65, 65, 65, 97, 97, 11, 11, 1, 1, 12, 12, 12, 12, 65] 201 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 345 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220333 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC(F)=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 169, 201, 201, 201, 169, 169, 169, 85, 85, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 169, 169, 169, 169, 201, 201, 85, 85, 12, 12, 1, 1, 1, 1, 169] 201 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 512 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220333 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC(F)=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 64, 64, 64, 64, 169, 169, 168, 169, 169, 169, 64, 1, 2, 2, 2, 3, 3, 11, 11, 65, 64, 169, 169, 169, 169, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 39] set([4, 5, 6, 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: 263 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220333 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220333 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220333/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220333 Building REAL300000220334 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220334' /scratch/stefan/7769801/working/building/REAL300000220334 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220334 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220334/0 /scratch/stefan/7769801/working/building/REAL300000220334 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/337 `/scratch/stefan/7769801/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=C(OC)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220334 none CCOC1=C(OC)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 47, 12, 12, 25, 25, 66, 25, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 25, 25, 25, 65, 142, 142, 142, 142, 142, 66, 66, 66, 25, 12, 12, 2, 2, 2, 3, 3, 1, 25, 65, 65, 65] 201 rigid atoms, others: [43, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 701 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220334 none CCOC1=C(OC)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 2, 1, 1, 1, 1, 3, 1, 1, 1, 3, 3, 25, 25, 25, 25, 25, 47, 93, 93, 25, 25, 25, 1, 1, 1, 3, 15, 15, 15, 14, 14, 4, 4, 4, 1, 3, 3, 25, 25, 25, 47, 47, 25, 1, 4, 4, 4] 201 rigid atoms, others: [2, 3, 4, 5, 7, 8, 9, 44, 35, 23, 24, 25] set([0, 1, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 393 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220334 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220334 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220334/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220334 Building REAL300000220335 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220335' /scratch/stefan/7769801/working/building/REAL300000220335 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220335 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220335/0 /scratch/stefan/7769801/working/building/REAL300000220335 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/338 `/scratch/stefan/7769801/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220335 none CC1=CC(F)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [21, 21, 21, 19, 21, 21, 21, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 21, 21, 21, 11, 11, 3, 3, 2, 2, 2, 1] 31 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 73 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: REAL300000220335 none CC1=CC(F)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 7, 7, 21, 21, 21, 21, 21, 31, 31, 31, 21, 21, 21, 2, 2, 2, 1, 1, 1, 7, 7, 31, 31, 21, 21, 21, 19] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220335 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220335 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220335/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220335 Building REAL300000220336 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220336' /scratch/stefan/7769801/working/building/REAL300000220336 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220336 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220336/0 /scratch/stefan/7769801/working/building/REAL300000220336 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/339 `/scratch/stefan/7769801/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CN=C2Cl)N1) `REAL300000220336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220336 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CN=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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, 31, 31, 31, 23, 23, 23, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 31, 31, 9, 9, 1, 1, 1, 21] 31 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 89 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: REAL300000220336 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CN=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 23, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 3, 11, 11, 23, 23, 23, 1] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 69 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220336 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220336 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220336/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220336 Building REAL300000220337 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220337' /scratch/stefan/7769801/working/building/REAL300000220337 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220337 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220337/0 /scratch/stefan/7769801/working/building/REAL300000220337 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/340 `/scratch/stefan/7769801/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)OC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC) `REAL300000220337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220337 none CCC(C)OC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 134, 111, 134, 36, 36, 36, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 36, 36, 36, 36, 88, 135, 135, 135, 135, 135, 134, 134, 134, 134, 36, 12, 12, 2, 2, 2, 3, 3, 1, 36, 36, 88, 88, 88] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 405 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220337 none CCC(C)OC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 11, 7, 11, 1, 1, 1, 1, 1, 5, 5, 36, 36, 36, 36, 36, 64, 104, 104, 36, 36, 36, 1, 1, 1, 1, 3, 12, 12, 12, 12, 12, 11, 11, 11, 11, 1, 5, 5, 36, 36, 36, 64, 64, 36, 1, 1, 4, 4, 4] 201 rigid atoms, others: [36, 5, 6, 7, 8, 45, 46, 25, 22, 23, 24, 4] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 417 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220337 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220337 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220337/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220337 Building REAL300000220338 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220338' /scratch/stefan/7769801/working/building/REAL300000220338 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220338 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220338/0 /scratch/stefan/7769801/working/building/REAL300000220338 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/341 `/scratch/stefan/7769801/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N=C(Cl)N2C)=N1) `REAL300000220338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220338 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N=C(Cl)N2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 16, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [40, 40, 40, 40, 49, 49, 49, 40, 40, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 49, 49, 40, 9, 9, 2, 2, 2] 49 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 118 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: REAL300000220338 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N=C(Cl)N2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 16, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 40, 40, 40, 40, 40, 40, 40, 1, 2, 2, 2, 3, 3, 1, 9, 9, 40, 40, 40] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 82 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220338 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220338 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220338/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220338 Building REAL300000220339 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220339' /scratch/stefan/7769801/working/building/REAL300000220339 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220339 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220339/0 /scratch/stefan/7769801/working/building/REAL300000220339 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/342 `/scratch/stefan/7769801/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CS2)N1) `REAL300000220339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220339 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [61, 61, 60, 60, 86, 104, 104, 60, 60, 60, 12, 12, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 60, 61, 61, 61, 86, 86, 12, 12, 7, 7, 1, 7, 7, 1, 61] 126 rigid atoms, others: [37, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 330 number of broken/clashed sets: 125 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220339 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [109, 109, 109, 109, 126, 126, 126, 109, 109, 109, 49, 49, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 109, 109, 109, 109, 126, 126, 49, 49, 1, 1, 1, 1, 1, 7, 109] 126 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 291 number of broken/clashed sets: 125 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220339 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 60, 60, 60, 109, 109, 61, 109, 109, 60, 60, 1, 2, 2, 2, 3, 3, 11, 11, 109, 109, 61, 109, 109, 60, 1] 126 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 307 number of broken/clashed sets: 125 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220339 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220339 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220339/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220339 Building REAL300000220340 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220340' /scratch/stefan/7769801/working/building/REAL300000220340 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220340 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220340/0 /scratch/stefan/7769801/working/building/REAL300000220340 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/343 `/scratch/stefan/7769801/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1C) `REAL300000220340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220340 none CCN1N=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', '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, 8, 8, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [80, 45, 45, 45, 45, 45, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 45, 45, 80, 80, 80, 80, 80, 45, 45, 45, 11, 11, 3, 3, 2, 2, 2, 1, 45, 45, 45] 106 rigid atoms, others: [38, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 278 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220340 none CCN1N=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', '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, 8, 8, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 45, 45, 45, 45, 45, 75, 76, 76, 45, 45, 45, 1, 1, 6, 6, 6, 6, 6, 2, 2, 2, 7, 7, 75, 75, 45, 45, 45, 45, 2, 2, 2] 106 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220340 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220340 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220340/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220340 Building REAL300000220341 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220341' /scratch/stefan/7769801/working/building/REAL300000220341 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220341 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220341/0 /scratch/stefan/7769801/working/building/REAL300000220341 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/344 `/scratch/stefan/7769801/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCCCC#N)=C2)=N1) `REAL300000220341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220341 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCCCC#N)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 49, 74, 74, 27, 27, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 7, 13, 13, 13, 1, 27, 27, 27, 27, 49, 49, 27, 5, 5, 1, 1, 1, 7, 7, 13, 13, 13, 13, 1] 201 rigid atoms, others: [34, 35, 36, 43, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 316 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220341 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCCCC#N)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 27, 27, 75, 82, 147, 147, 147, 27, 1, 2, 2, 2, 3, 3, 1, 9, 9, 27, 27, 27, 82, 82, 147, 147, 147, 147, 27] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 513 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220341 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220341 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220341/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220341 Building REAL300000220342 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220342' /scratch/stefan/7769801/working/building/REAL300000220342 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220342 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220342/0 /scratch/stefan/7769801/working/building/REAL300000220342 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/345 `/scratch/stefan/7769801/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC=CC2=CC=CC=C2[N+](=O)[O-])=N1) `REAL300000220342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220342 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC=CC2=CC=CC=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [61, 61, 61, 61, 83, 83, 83, 61, 61, 61, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 61, 61, 61, 61, 83, 83, 61, 13, 13, 7, 7, 1, 1, 1, 1] 83 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 231 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220342 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC=CC2=CC=CC=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 29, 29, 61, 61, 61, 61, 61, 61, 61, 61, 1, 2, 2, 2, 3, 3, 1, 11, 11, 29, 29, 61, 61, 61, 61] 83 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 161 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220342 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220342 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220342/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220342 Building REAL300000220343 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220343' /scratch/stefan/7769801/working/building/REAL300000220343 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220343 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220343/0 /scratch/stefan/7769801/working/building/REAL300000220343 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/346 `/scratch/stefan/7769801/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3O2)N1) `REAL300000220343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220343 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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, 25, 25, 37, 37, 37, 25, 25, 25, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 37, 37, 12, 11, 1, 1, 1, 1, 1, 26] 37 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 119 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: REAL300000220343 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 11, 11, 26, 26, 25, 25, 26, 1] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220343 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220343 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220343/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220343 Building REAL300000220344 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220344' /scratch/stefan/7769801/working/building/REAL300000220344 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220344 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220344/0 /scratch/stefan/7769801/working/building/REAL300000220344 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/347 `/scratch/stefan/7769801/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N+](=O)[O-])C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220344 none CCOC1=CC=C([N+](=O)[O-])C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', '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, 1, 8, 11, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 128, 66, 66, 66, 36, 66, 66, 66, 66, 66, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 152, 152, 152, 152, 152, 66, 66, 66, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 470 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220344 none CCOC1=CC=C([N+](=O)[O-])C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', '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, 1, 8, 11, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 66, 66, 66, 66, 66, 118, 162, 162, 66, 66, 66, 24, 24, 24, 24, 24, 1, 1, 1, 9, 9, 66, 66, 66, 118, 118, 66] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 638 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220344 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220344 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220344/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220344 Building REAL300000220345 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220345' /scratch/stefan/7769801/working/building/REAL300000220345 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220345 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220345/0 /scratch/stefan/7769801/working/building/REAL300000220345 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/348 `/scratch/stefan/7769801/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=C(F)C(F)=C2)=N1) `REAL300000220345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220345 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=C(F)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [13, 13, 13, 13, 15, 15, 15, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 15, 15, 13, 4, 4, 1, 1] 15 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 33 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: REAL300000220345 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=C(F)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 13, 13, 13, 9, 9, 13, 13, 13, 1, 2, 2, 2, 3, 3, 1, 9, 9, 13, 13] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 63 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220345 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220345 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220345/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220345 Building REAL300000220346 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220346' /scratch/stefan/7769801/working/building/REAL300000220346 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220346 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220346/0 /scratch/stefan/7769801/working/building/REAL300000220346 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/349 `/scratch/stefan/7769801/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(C(F)(F)F)=C2)=N1) `REAL300000220346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220346 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 24, 24, 24, 33, 33, 33, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 24, 24, 24, 24, 33, 33, 24, 5, 5, 1, 1, 1] 33 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 94 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220346 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 24, 24, 23, 24, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 3, 1, 9, 9, 24, 24, 24] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 70 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220346 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220346 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220346/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220346 Building REAL300000220347 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220347' /scratch/stefan/7769801/working/building/REAL300000220347 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220347 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220347/0 /scratch/stefan/7769801/working/building/REAL300000220347 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/350 `/scratch/stefan/7769801/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N(C)C)C(F)=C2)N1) `REAL300000220347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220347 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N(C)C)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 59, 69, 69, 32, 32, 32, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 1, 32, 32, 32, 32, 59, 59, 6, 6, 1, 1, 7, 7, 7, 7, 7, 7, 1, 32] 69 rigid atoms, others: [32, 39, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 259 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220347 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N(C)C)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 32, 32, 30, 32, 59, 59, 32, 32, 32, 1, 2, 2, 2, 3, 3, 11, 11, 32, 32, 59, 59, 59, 59, 59, 59, 32, 1] 69 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 40, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 180 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220347 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220347 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220347/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220347 Building REAL300000220348 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220348' /scratch/stefan/7769801/working/building/REAL300000220348 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220348 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220348/0 /scratch/stefan/7769801/working/building/REAL300000220348 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/351 `/scratch/stefan/7769801/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C(F)=C2)=N1) `REAL300000220348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220348 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 64, 98, 98, 39, 39, 39, 7, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 39, 39, 39, 39, 64, 64, 39, 7, 7, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1] 116 rigid atoms, others: [45, 35, 36, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 346 number of broken/clashed sets: 116 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220348 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 116, 116, 116, 83, 83, 83, 34, 34, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 83, 83, 83, 83, 116, 116, 83, 34, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9] 116 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45]) total number of confs: 364 number of broken/clashed sets: 116 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220348 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 39, 39, 38, 39, 83, 83, 83, 83, 83, 39, 39, 39, 1, 2, 2, 2, 3, 3, 1, 11, 11, 39, 39, 83, 83, 83, 83, 83, 83, 83, 83, 39] 116 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220348 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220348 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220348/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220348 Building REAL300000220349 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220349' /scratch/stefan/7769801/working/building/REAL300000220349 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220349 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220349/0 /scratch/stefan/7769801/working/building/REAL300000220349 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/352 `/scratch/stefan/7769801/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl) `REAL300000220349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220349 none C=CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 147, 92, 29, 27, 29, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 29, 29, 155, 155, 155, 147, 147, 29, 29, 9, 9, 2, 2, 2, 3, 3, 1, 29] 201 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 505 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220349 none C=CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 5, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 52, 86, 86, 29, 29, 29, 1, 1, 1, 30, 30, 30, 20, 20, 1, 1, 5, 5, 29, 29, 29, 52, 52, 29, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 40, 22, 23, 24, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 415 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220349 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220349 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220349/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220349 Building REAL300000220350 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220350' /scratch/stefan/7769801/working/building/REAL300000220350 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220350 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220350/0 /scratch/stefan/7769801/working/building/REAL300000220350 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/353 `/scratch/stefan/7769801/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(F)(F)F)=C2)=N1) `REAL300000220350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220350 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 51, 82, 82, 28, 28, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 13, 13, 13, 1, 28, 28, 28, 28, 51, 51, 28, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 323 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220350 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 28, 28, 28, 28, 28, 136, 136, 136, 136, 28, 1, 2, 2, 2, 3, 3, 1, 9, 9, 28, 28, 28, 28] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 204 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220350 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220350 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220350/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220350 Building REAL300000220351 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220351' /scratch/stefan/7769801/working/building/REAL300000220351 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220351 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220351/0 /scratch/stefan/7769801/working/building/REAL300000220351 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/354 `/scratch/stefan/7769801/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C2OC(C)CC2=C1) `REAL300000220351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220351 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C2OC(C)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [75, 52, 52, 52, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 75, 75, 75, 52, 12, 12, 3, 3, 2, 2, 2, 1, 52, 52, 52, 52, 52, 52, 52] 110 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) 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: REAL300000220351 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C2OC(C)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 11, 11, 52, 52, 52, 52, 52, 78, 110, 110, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 11, 11, 78, 78, 52, 52, 52, 52, 1, 2, 2, 2, 1, 1, 1] 110 rigid atoms, others: [1, 2, 3, 4, 5, 38, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 367 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220351 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220351 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220351/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220351 Building REAL300000220352 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220352' /scratch/stefan/7769801/working/building/REAL300000220352 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220352 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220352/0 /scratch/stefan/7769801/working/building/REAL300000220352 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/355 `/scratch/stefan/7769801/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)S2)N1) `REAL300000220352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220352 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [40, 40, 40, 40, 48, 48, 48, 39, 40, 39, 12, 12, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 40, 40, 40, 40, 48, 48, 12, 12, 1, 4, 4, 3, 4, 4, 40] 48 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220352 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [41, 41, 41, 41, 48, 48, 48, 41, 41, 40, 23, 23, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 41, 41, 41, 41, 48, 48, 23, 23, 3, 1, 1, 1, 1, 1, 41] 48 rigid atoms, others: [33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 122 number of broken/clashed sets: 47 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220352 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 40, 40, 40, 40, 41, 41, 41, 41, 40, 40, 1, 2, 2, 2, 3, 3, 10, 10, 40, 41, 41, 41, 40, 41, 1] 48 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 94 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220352 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220352 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220352/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220352 Building REAL300000220353 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220353' /scratch/stefan/7769801/working/building/REAL300000220353 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220353 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220353/0 /scratch/stefan/7769801/working/building/REAL300000220353 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/356 `/scratch/stefan/7769801/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CCCl)N=C2)=N1) `REAL300000220353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220353 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CCCl)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'Cl', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 16, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 62, 102, 102, 39, 39, 39, 7, 7, 1, 1, 1, 1, 1, 7, 11, 1, 1, 39, 39, 39, 39, 62, 62, 39, 7, 7, 1, 7, 7, 11, 11, 1] 201 rigid atoms, others: [35, 12, 13, 14, 15, 16, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 392 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220353 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CCCl)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'Cl', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 16, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 114, 151, 39, 39, 1, 2, 2, 2, 3, 3, 1, 11, 11, 39, 114, 114, 151, 151, 39] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 607 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220353 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220353 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220353/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220353 Building REAL300000220354 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220354' /scratch/stefan/7769801/working/building/REAL300000220354 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220354 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220354/0 /scratch/stefan/7769801/working/building/REAL300000220354 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/357 `/scratch/stefan/7769801/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CN2)N1) `REAL300000220354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220354 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CN2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 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: [53, 53, 53, 53, 80, 101, 101, 53, 53, 53, 12, 12, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 53, 54, 54, 54, 80, 80, 12, 12, 7, 7, 1, 7, 7, 1, 1, 53] 101 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 340 number of broken/clashed sets: 100 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220354 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CN2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 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: [91, 91, 91, 91, 101, 101, 101, 91, 91, 91, 46, 46, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 91, 91, 91, 91, 101, 101, 46, 46, 1, 1, 1, 1, 1, 7, 7, 91] 101 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 227 number of broken/clashed sets: 100 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220354 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CN2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 53, 53, 53, 91, 91, 74, 91, 91, 53, 53, 1, 2, 2, 2, 3, 3, 12, 12, 91, 91, 75, 91, 91, 53, 53, 1] 101 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 216 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220354 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220354 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220354/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220354 Building REAL300000220355 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220355' /scratch/stefan/7769801/working/building/REAL300000220355 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220355 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220355/0 /scratch/stefan/7769801/working/building/REAL300000220355 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/358 `/scratch/stefan/7769801/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OCC#N)=C2)N1) `REAL300000220355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220355 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OCC#N)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 58, 84, 84, 33, 33, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 1, 33, 33, 33, 33, 58, 58, 5, 5, 1, 1, 1, 13, 13, 1, 33] 201 rigid atoms, others: [32, 33, 36, 12, 13, 14, 15, 16, 17, 18, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 37]) total number of confs: 338 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220355 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OCC#N)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 33, 33, 33, 33, 33, 86, 128, 128, 33, 1, 2, 2, 2, 3, 3, 12, 12, 33, 33, 33, 128, 128, 33, 1] 201 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 395 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220355 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220355 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220355/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220355 Building REAL300000220356 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220356' /scratch/stefan/7769801/working/building/REAL300000220356 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220356 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220356/0 /scratch/stefan/7769801/working/building/REAL300000220356 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/359 `/scratch/stefan/7769801/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=N2)N1) `REAL300000220356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220356 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [33, 33, 32, 32, 43, 43, 43, 32, 32, 32, 10, 10, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 33, 33, 33, 33, 43, 43, 11, 10, 1, 4, 4, 3, 4, 4, 33] 43 rigid atoms, others: [32, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 132 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220356 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [33, 33, 33, 33, 43, 43, 43, 33, 33, 33, 23, 23, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 33, 33, 33, 33, 43, 43, 23, 23, 4, 1, 1, 1, 1, 1, 33] 43 rigid atoms, others: [33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 124 number of broken/clashed sets: 42 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220356 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 32, 32, 32, 33, 33, 33, 33, 33, 32, 32, 1, 2, 2, 2, 3, 3, 9, 9, 33, 33, 33, 33, 33, 33, 1] 43 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220356 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220356 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220356/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220356 Building REAL300000220357 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220357' /scratch/stefan/7769801/working/building/REAL300000220357 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220357 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220357/0 /scratch/stefan/7769801/working/building/REAL300000220357 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/360 `/scratch/stefan/7769801/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(C)C#N)C=C2)=N1) `REAL300000220357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220357 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(C)C#N)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 8, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 40, 65, 65, 24, 24, 24, 4, 4, 1, 1, 1, 1, 1, 1, 11, 40, 40, 40, 1, 1, 24, 24, 24, 24, 40, 40, 24, 4, 4, 1, 1, 40, 40, 40, 40, 1, 1] 201 rigid atoms, others: [33, 34, 39, 40, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 356 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220357 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(C)C#N)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 8, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 13, 13, 24, 24, 13, 13, 103, 151, 151, 151, 24, 24, 1, 2, 2, 2, 3, 3, 1, 13, 13, 24, 24, 151, 151, 151, 151, 24, 24] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 470 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220357 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220357 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220357/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220357 Building REAL300000220358 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220358' /scratch/stefan/7769801/working/building/REAL300000220358 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220358 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220358/0 /scratch/stefan/7769801/working/building/REAL300000220358 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/361 `/scratch/stefan/7769801/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=CN2CC(F)(F)F)=N1) `REAL300000220358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220358 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=CN2CC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 60, 61, 61, 103, 134, 134, 61, 61, 61, 10, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 60, 61, 61, 61, 103, 103, 60, 10, 10, 1, 1, 6, 6] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 477 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220358 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=CN2CC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 61, 61, 61, 61, 61, 141, 141, 141, 141, 1, 2, 2, 2, 3, 3, 1, 12, 12, 61, 61, 141, 141] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 465 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220358 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220358 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220358/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220358 Building REAL300000220359 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220359' /scratch/stefan/7769801/working/building/REAL300000220359 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220359 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220359/0 /scratch/stefan/7769801/working/building/REAL300000220359 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/362 `/scratch/stefan/7769801/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C4OCOC4=C3)=N2)=N1) `REAL300000220359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220359 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C4OCOC4=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [66, 66, 66, 66, 97, 106, 106, 66, 66, 66, 12, 12, 1, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 5, 5, 1, 66, 67, 67, 67, 97, 97, 62, 13, 12, 1, 5, 5, 5, 5, 5] 127 rigid atoms, others: [36, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 330 number of broken/clashed sets: 126 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220359 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C4OCOC4=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [111, 111, 111, 111, 127, 127, 127, 111, 111, 111, 38, 38, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 111, 111, 111, 111, 127, 127, 109, 38, 38, 5, 1, 1, 1, 1, 1] 127 rigid atoms, others: [37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 278 number of broken/clashed sets: 126 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220359 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C4OCOC4=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 66, 66, 66, 66, 111, 111, 111, 111, 111, 111, 111, 111, 66, 1, 2, 2, 2, 3, 3, 1, 12, 12, 66, 111, 111, 111, 111, 111] 127 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 195 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220359 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220359 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220359/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220359 Building REAL300000220360 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220360' /scratch/stefan/7769801/working/building/REAL300000220360 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220360 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220360/0 /scratch/stefan/7769801/working/building/REAL300000220360 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/363 `/scratch/stefan/7769801/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CS3)=N2)=N1) `REAL300000220360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220360 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CS3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 66, 92, 131, 131, 67, 67, 67, 11, 11, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 67, 67, 67, 67, 92, 92, 61, 11, 11, 1, 12, 12, 12] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 420 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220360 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CS3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 170, 170, 201, 201, 201, 170, 170, 170, 57, 57, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 170, 170, 170, 170, 201, 201, 168, 57, 56, 12, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 458 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220360 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CS3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 67, 170, 170, 170, 170, 66, 1, 2, 2, 2, 3, 3, 1, 12, 12, 67, 170, 170, 170] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 260 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220360 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220360 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220360/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220360 Building REAL300000220361 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220361' /scratch/stefan/7769801/working/building/REAL300000220361 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220361 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220361/0 /scratch/stefan/7769801/working/building/REAL300000220361 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/364 `/scratch/stefan/7769801/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3N=CC=CN23)N1) `REAL300000220361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220361 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3N=CC=CN23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [33, 33, 33, 33, 44, 44, 44, 33, 33, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 44, 44, 11, 11, 1, 1, 1, 1, 33] 44 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 118 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: REAL300000220361 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3N=CC=CN23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 33, 33, 33, 33, 33, 33, 33, 33, 1, 2, 2, 2, 3, 3, 10, 10, 33, 33, 33, 33, 1] 44 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220361 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220361 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220361/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220361 Building REAL300000220362 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220362' /scratch/stefan/7769801/working/building/REAL300000220362 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220362 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220362/0 /scratch/stefan/7769801/working/building/REAL300000220362 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/365 `/scratch/stefan/7769801/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC3=CC=CC=C23)N1) `REAL300000220362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220362 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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: [31, 31, 31, 31, 41, 41, 41, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 41, 41, 9, 9, 1, 1, 1, 1, 1, 1, 31] 41 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 107 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220362 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 9, 9, 31, 31, 31, 31, 31, 31, 1] 41 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 73 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220362 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220362 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220362/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220362 Building REAL300000220363 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220363' /scratch/stefan/7769801/working/building/REAL300000220363 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220363 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220363/0 /scratch/stefan/7769801/working/building/REAL300000220363 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/366 `/scratch/stefan/7769801/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C(Cl)=C2)=N1) `REAL300000220363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220363 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 58, 104, 104, 30, 30, 30, 5, 5, 1, 1, 1, 1, 1, 1, 7, 27, 27, 1, 1, 1, 30, 30, 30, 30, 58, 58, 30, 5, 5, 1, 1, 27, 1] 201 rigid atoms, others: [33, 34, 36, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 475 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220363 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 30, 30, 28, 30, 106, 170, 170, 30, 30, 30, 1, 2, 2, 2, 3, 3, 1, 9, 9, 30, 30, 170, 30] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 539 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220363 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220363 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220363/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220363 Building REAL300000220364 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220364' /scratch/stefan/7769801/working/building/REAL300000220364 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220364 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220364/0 /scratch/stefan/7769801/working/building/REAL300000220364 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/367 `/scratch/stefan/7769801/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)S1) `REAL300000220364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220364 none CCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.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, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [106, 46, 46, 46, 46, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 46, 106, 106, 106, 106, 106, 46, 46, 12, 12, 3, 3, 2, 2, 2, 1] 118 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 375 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220364 none CCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.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, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 12, 12, 46, 46, 46, 46, 46, 60, 72, 72, 46, 46, 46, 1, 9, 9, 9, 8, 8, 1, 1, 12, 12, 60, 60, 46, 46, 46, 46] 118 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 230 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220364 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220364 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220364/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220364 Building REAL300000220365 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220365' /scratch/stefan/7769801/working/building/REAL300000220365 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220365 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220365/0 /scratch/stefan/7769801/working/building/REAL300000220365 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/368 `/scratch/stefan/7769801/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=N1) `REAL300000220365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220365 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [66, 65, 66, 66, 93, 97, 97, 66, 66, 66, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 6, 6, 7, 7, 1, 65, 66, 66, 66, 93, 93, 66, 13, 13, 1, 1, 7, 7, 7, 7] 139 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 300 number of broken/clashed sets: 138 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220365 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [115, 115, 115, 115, 139, 139, 139, 115, 115, 115, 49, 49, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 115, 115, 115, 115, 139, 139, 115, 49, 49, 7, 7, 1, 1, 1, 1] 139 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 342 number of broken/clashed sets: 138 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220365 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 66, 66, 66, 66, 115, 115, 68, 66, 115, 115, 115, 115, 66, 1, 2, 2, 2, 3, 3, 1, 12, 12, 66, 66, 115, 115, 115, 115] 139 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 455 number of broken/clashed sets: 138 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220365 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220365 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220365/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220365 Building REAL300000220366 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220366' /scratch/stefan/7769801/working/building/REAL300000220366 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220366 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220366/0 /scratch/stefan/7769801/working/building/REAL300000220366 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/369 `/scratch/stefan/7769801/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1F) `REAL300000220366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220366 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [17, 16, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 2, 2, 2, 1, 17] 29 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) 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: REAL300000220366 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 5, 5, 17, 17, 17, 17, 17, 29, 29, 29, 17, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 5, 5, 29, 29, 17, 17, 17, 17, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220366 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220366 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220366/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220366 Building REAL300000220367 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220367' /scratch/stefan/7769801/working/building/REAL300000220367 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220367 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220367/0 /scratch/stefan/7769801/working/building/REAL300000220367 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/370 `/scratch/stefan/7769801/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC(Cl)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N1C) `REAL300000220367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220367 none COC1=NC(Cl)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [60, 42, 42, 42, 42, 42, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 42, 42, 60, 60, 60, 11, 11, 2, 2, 2, 3, 3, 1, 42, 42, 42] 79 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 124 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220367 none COC1=NC(Cl)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 1, 1, 1, 1, 1, 8, 8, 42, 42, 42, 42, 42, 72, 79, 79, 42, 42, 42, 1, 1, 7, 7, 7, 8, 8, 42, 42, 42, 72, 72, 42, 2, 2, 2] 79 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 281 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220367 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220367 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220367/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220367 Building REAL300000220368 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220368' /scratch/stefan/7769801/working/building/REAL300000220368 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220368 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220368/0 /scratch/stefan/7769801/working/building/REAL300000220368 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/371 `/scratch/stefan/7769801/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220368 none CC1=CC=CC=C1C1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 43, 43, 44, 44, 44, 71, 76, 76, 44, 44, 44, 1, 7, 7, 7, 7, 2, 7, 7, 1, 1, 1, 6, 6, 71, 71, 44, 44, 44, 44, 1] 152 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 45, 26] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 258 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220368 none CC1=CC=CC=C1C1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 60, 114, 114, 44, 44, 43, 44, 44, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 44, 114, 114, 114, 114, 80, 114, 114, 43, 44, 44, 12, 12, 3, 3, 2, 2, 2, 1, 44] 152 rigid atoms, others: [44, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45]) total number of confs: 337 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220368 none CC1=CC=CC=C1C1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 29, 29, 114, 114, 114, 114, 114, 152, 152, 152, 114, 114, 114, 7, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 29, 29, 152, 152, 114, 114, 114, 114, 7] 152 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 407 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220368 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220368 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220368/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220368 Building REAL300000220369 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220369' /scratch/stefan/7769801/working/building/REAL300000220369 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220369 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220369/0 /scratch/stefan/7769801/working/building/REAL300000220369 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/372 `/scratch/stefan/7769801/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=COC(C3=CC=CC=C3)=N2)N1) `REAL300000220369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220369 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=COC(C3=CC=CC=C3)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [45, 45, 45, 45, 52, 52, 52, 44, 45, 44, 13, 13, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 45, 45, 45, 45, 52, 52, 13, 13, 1, 4, 4, 2, 4, 4, 45] 52 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220369 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=COC(C3=CC=CC=C3)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [46, 46, 46, 46, 52, 52, 52, 46, 46, 46, 25, 25, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 46, 46, 46, 46, 52, 52, 25, 25, 3, 1, 1, 1, 1, 1, 46] 52 rigid atoms, others: [33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 126 number of broken/clashed sets: 51 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220369 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=COC(C3=CC=CC=C3)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 45, 45, 45, 45, 46, 46, 46, 46, 46, 45, 1, 2, 2, 2, 3, 3, 11, 11, 45, 46, 46, 46, 46, 46, 1] 52 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220369 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220369 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220369/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220369 Building REAL300000220370 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220370' /scratch/stefan/7769801/working/building/REAL300000220370 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220370 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220370/0 /scratch/stefan/7769801/working/building/REAL300000220370 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/373 `/scratch/stefan/7769801/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OC(C)(C)CC3=C2)N1) `REAL300000220370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220370 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OC(C)(C)CC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 24, 24, 24, 29, 29, 29, 24, 24, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 29, 29, 6, 6, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 24] 29 rigid atoms, others: [32, 33, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 43]) total number of confs: 79 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220370 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OC(C)(C)CC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 3, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 43, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 70 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220370 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220370 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220370/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220370 Building REAL300000220371 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220371' /scratch/stefan/7769801/working/building/REAL300000220371 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220371 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220371/0 /scratch/stefan/7769801/working/building/REAL300000220371 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/374 `/scratch/stefan/7769801/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1F) `REAL300000220371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220371 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 16, 16, 5, 9, 16, 16, 16, 16, 5, 5, 3, 3, 1, 1, 1, 1, 16, 16] 29 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 73 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: REAL300000220371 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 5, 5, 16, 16, 16, 16, 16, 29, 29, 29, 16, 16, 16, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 29, 29, 16, 16, 16, 16, 1, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220371 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220371 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220371/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220371 Building REAL300000220372 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220372' /scratch/stefan/7769801/working/building/REAL300000220372 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220372 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220372/0 /scratch/stefan/7769801/working/building/REAL300000220372 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/375 `/scratch/stefan/7769801/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(F)=C2F)N1) `REAL300000220372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220372 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(F)=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [39, 39, 39, 39, 43, 43, 43, 39, 39, 39, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 43, 43, 9, 9, 1, 1, 1, 35] 43 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 85 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: REAL300000220372 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(F)=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 3, 3, 11, 11, 39, 39, 39, 1] 43 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 83 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220372 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220372 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220372/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220372 Building REAL300000220373 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220373' /scratch/stefan/7769801/working/building/REAL300000220373 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220373 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220373/0 /scratch/stefan/7769801/working/building/REAL300000220373 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/376 `/scratch/stefan/7769801/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Cl)=C1OC) `REAL300000220373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220373 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Cl', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [85, 52, 52, 52, 52, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 52, 52, 52, 52, 82, 85, 85, 85, 52, 52, 12, 12, 2, 2, 2, 3, 3, 1, 82, 82, 82] 116 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 218 number of broken/clashed sets: 116 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220373 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Cl', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 52, 52, 52, 52, 52, 76, 88, 88, 52, 52, 52, 1, 1, 1, 1, 5, 4, 4, 4, 1, 1, 9, 9, 52, 52, 52, 76, 76, 52, 6, 6, 6] 116 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 283 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220373 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220373 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220373/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220373 Building REAL300000220374 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220374' /scratch/stefan/7769801/working/building/REAL300000220374 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220374 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220374/0 /scratch/stefan/7769801/working/building/REAL300000220374 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/377 `/scratch/stefan/7769801/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220374 none COCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 125, 80, 71, 20, 20, 36, 36, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 36, 36, 140, 140, 140, 125, 125, 80, 80, 36, 36, 11, 11, 2, 2, 2, 3, 3, 1, 36, 36] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 492 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220374 none COCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 10, 6, 4, 1, 1, 1, 1, 1, 1, 5, 5, 36, 36, 36, 36, 36, 60, 100, 100, 36, 36, 36, 1, 1, 22, 22, 22, 10, 10, 6, 6, 1, 1, 5, 5, 36, 36, 36, 60, 60, 36, 1, 1] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 42, 43, 23, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 397 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220374 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220374 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220374/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220374 Building REAL300000220375 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220375' /scratch/stefan/7769801/working/building/REAL300000220375 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220375 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220375/0 /scratch/stefan/7769801/working/building/REAL300000220375 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/378 `/scratch/stefan/7769801/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N=C3C=CSC3=C2)N1) `REAL300000220375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220375 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N=C3C=CSC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 14, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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: [27, 27, 27, 27, 37, 37, 37, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 37, 37, 9, 9, 1, 1, 1, 27] 37 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 105 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: REAL300000220375 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N=C3C=CSC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 14, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 11, 11, 27, 27, 27, 1] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 73 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220375 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220375 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220375/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220375 Building REAL300000220376 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220376' /scratch/stefan/7769801/working/building/REAL300000220376 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220376 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220376/0 /scratch/stefan/7769801/working/building/REAL300000220376 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/379 `/scratch/stefan/7769801/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(C)C)C=C2)=N1) `REAL300000220376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220376 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(C)C)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 37, 59, 59, 24, 24, 24, 4, 4, 1, 1, 1, 1, 1, 1, 7, 19, 24, 30, 1, 1, 24, 24, 24, 24, 37, 37, 24, 4, 4, 1, 1, 19, 19, 30, 30, 30, 30, 30, 30, 30, 1, 1] 201 rigid atoms, others: [33, 34, 44, 45, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 354 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220376 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(C)C)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 13, 13, 24, 24, 13, 13, 70, 120, 133, 141, 24, 24, 1, 2, 2, 2, 3, 3, 1, 13, 13, 24, 24, 120, 120, 141, 141, 141, 141, 141, 141, 141, 24, 24] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 597 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220376 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220376 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220376/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220376 Building REAL300000220377 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220377' /scratch/stefan/7769801/working/building/REAL300000220377 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220377 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220377/0 /scratch/stefan/7769801/working/building/REAL300000220377 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/380 `/scratch/stefan/7769801/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220377 none CC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 54, 54, 54, 53, 53, 94, 102, 102, 54, 54, 54, 11, 11, 11, 11, 1, 11, 11, 1, 1, 11, 11, 94, 94, 54, 54, 54, 54, 11] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 376 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220377 none CC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 54, 123, 123, 54, 54, 54, 54, 53, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 123, 123, 123, 123, 81, 123, 123, 53, 54, 11, 11, 3, 3, 2, 2, 2, 1, 123] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 411 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220377 none CC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 45, 45, 123, 123, 123, 123, 123, 201, 201, 201, 123, 123, 123, 1, 2, 2, 2, 1, 1, 1, 11, 11, 45, 45, 201, 201, 123, 123, 123, 123, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 25, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 674 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220377 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220377 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220377/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220377 Building REAL300000220378 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220378' /scratch/stefan/7769801/working/building/REAL300000220378 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220378 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220378/0 /scratch/stefan/7769801/working/building/REAL300000220378 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/381 `/scratch/stefan/7769801/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1[N+](=O)[O-]) `REAL300000220378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220378 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 3, 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: [50, 10, 10, 33, 33, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 33, 33, 33, 33, 33, 50, 50, 50, 33, 33, 10, 10, 3, 3, 2, 2, 2, 1, 33] 64 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 170 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: REAL300000220378 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 3, 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: [3, 1, 1, 1, 1, 1, 1, 5, 5, 33, 33, 33, 33, 33, 55, 64, 64, 33, 33, 33, 1, 1, 1, 2, 2, 4, 4, 4, 1, 1, 5, 5, 55, 55, 33, 33, 33, 33, 1] 64 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 38, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 224 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220378 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220378 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220378/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220378 Building REAL300000220379 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220379' /scratch/stefan/7769801/working/building/REAL300000220379 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220379 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220379/0 /scratch/stefan/7769801/working/building/REAL300000220379 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/382 `/scratch/stefan/7769801/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC(=O)[O-])=C2)=N1) `REAL300000220379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220379 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 51, 86, 86, 33, 33, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 14, 27, 27, 1, 33, 33, 33, 33, 51, 51, 33, 5, 5, 1, 1, 1, 14, 14, 1] 201 rigid atoms, others: [33, 34, 35, 38, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 375 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220379 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 33, 33, 33, 33, 33, 115, 148, 166, 166, 33, 1, 2, 2, 2, 3, 3, 1, 12, 12, 33, 33, 33, 148, 148, 33] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 441 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220379 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220379 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220379/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220379 Building REAL300000220380 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220380' /scratch/stefan/7769801/working/building/REAL300000220380 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220380 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220380/0 /scratch/stefan/7769801/working/building/REAL300000220380 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/383 `/scratch/stefan/7769801/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(F)(F)F)=CC=C2F)=N1) `REAL300000220380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220380 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(F)(F)F)=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 39, 39, 39, 51, 51, 51, 39, 39, 39, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 39, 39, 39, 39, 51, 51, 39, 11, 11, 1, 1, 1] 51 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 137 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220380 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(F)(F)F)=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 39, 39, 39, 17, 39, 39, 39, 1, 2, 2, 2, 3, 3, 1, 11, 11, 39, 39, 39] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 158 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220380 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220380 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220380/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220380 Building REAL300000220381 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220381' /scratch/stefan/7769801/working/building/REAL300000220381 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220381 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220381/0 /scratch/stefan/7769801/working/building/REAL300000220381 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/384 `/scratch/stefan/7769801/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC1=CC=CN=C1) `REAL300000220381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220381 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 24, 24, 15, 15, 87, 136, 136, 136, 136, 136, 24, 24, 24, 24, 9, 9, 2, 2, 2, 3, 3, 1, 24, 24, 136, 136, 136, 136] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 39] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 269 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220381 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 8, 8, 41, 41, 126, 126, 126, 126, 126, 189, 191, 191, 126, 126, 126, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 41, 41, 126, 126, 126, 189, 189, 126, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 619 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220381 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 24, 24, 24, 24, 24, 40, 66, 66, 24, 24, 24, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 2, 2, 2, 1, 5, 5, 24, 24, 24, 40, 40, 24, 1, 1, 14, 14, 14, 14] 201 rigid atoms, others: [0, 1, 2, 3, 4, 40, 41, 18, 19, 20, 21, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 259 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220381 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220381 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220381/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220381 Building REAL300000220382 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220382' /scratch/stefan/7769801/working/building/REAL300000220382 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220382 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220382/0 /scratch/stefan/7769801/working/building/REAL300000220382 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/385 `/scratch/stefan/7769801/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(Cl)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220382 none COC1=CC=CC(Cl)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [62, 54, 54, 54, 21, 54, 54, 54, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 62, 62, 62, 54, 53, 54, 11, 11, 3, 3, 2, 2, 2, 1] 79 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220382 none COC1=CC=CC(Cl)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 54, 54, 54, 54, 54, 79, 79, 79, 54, 54, 54, 4, 4, 4, 1, 1, 1, 9, 9, 79, 79, 54, 54, 54, 54] 79 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220382 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220382 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220382/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220382 Building REAL300000220383 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220383' /scratch/stefan/7769801/working/building/REAL300000220383 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220383 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220383/0 /scratch/stefan/7769801/working/building/REAL300000220383 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/386 `/scratch/stefan/7769801/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220383 none CC1=CC=C(F)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [33, 33, 18, 33, 33, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 33, 33, 33, 33, 33, 33, 9, 9, 3, 3, 2, 2, 2, 1, 33] 43 rigid atoms, others: [34, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 129 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: REAL300000220383 none CC1=CC=C(F)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 33, 33, 33, 33, 33, 43, 43, 43, 33, 33, 33, 1, 2, 2, 2, 1, 1, 11, 11, 43, 43, 33, 33, 33, 31, 1] 43 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220383 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220383 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220383/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220383 Building REAL300000220384 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220384' /scratch/stefan/7769801/working/building/REAL300000220384 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220384 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220384/0 /scratch/stefan/7769801/working/building/REAL300000220384 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/387 `/scratch/stefan/7769801/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC(F)F)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220384 none COC1=CC=C(OC(F)F)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 47, 47, 47, 47, 47, 47, 95, 121, 121, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 47, 75, 75, 75, 47, 47, 121, 11, 11, 2, 2, 2, 3, 3, 1, 47] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 378 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220384 none COC1=CC=C(OC(F)F)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 23, 23, 1, 1, 7, 7, 47, 47, 47, 47, 47, 71, 119, 119, 47, 47, 47, 1, 3, 3, 3, 1, 1, 23, 7, 7, 47, 47, 47, 71, 71, 47, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 10, 11, 25, 29, 30] set([0, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 463 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220384 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220384 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220384/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220384 Building REAL300000220385 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220385' /scratch/stefan/7769801/working/building/REAL300000220385 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220385 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220385/0 /scratch/stefan/7769801/working/building/REAL300000220385 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/388 `/scratch/stefan/7769801/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C(C)C)N=C2)N1) `REAL300000220385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220385 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C(C)C)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 71, 98, 98, 42, 43, 42, 7, 7, 1, 1, 1, 1, 1, 13, 13, 1, 1, 43, 43, 43, 43, 71, 71, 7, 7, 1, 13, 13, 13, 13, 13, 13, 13, 1, 43] 104 rigid atoms, others: [37, 12, 13, 14, 15, 16, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 367 number of broken/clashed sets: 103 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220385 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C(C)C)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 43, 43, 43, 103, 103, 43, 43, 1, 2, 2, 2, 3, 3, 11, 11, 43, 103, 103, 103, 103, 103, 103, 103, 43, 1] 104 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 359 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220385 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220385 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220385/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220385 Building REAL300000220386 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220386' /scratch/stefan/7769801/working/building/REAL300000220386 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220386 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220386/0 /scratch/stefan/7769801/working/building/REAL300000220386 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/389 `/scratch/stefan/7769801/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C1=NC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1)C1CC1) `REAL300000220386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220386 none CC(=O)N(C1=NC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.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, 1, 11, 8, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 107, 148, 43, 42, 42, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 43, 43, 107, 154, 154, 148, 148, 148, 12, 12, 2, 2, 2, 3, 3, 1, 43, 154, 154, 154, 154, 154] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 603 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220386 none CC(=O)N(C1=NC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.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, 1, 11, 8, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 11, 1, 6, 14, 14, 14, 41, 41, 154, 154, 154, 154, 154, 192, 193, 193, 154, 154, 154, 14, 14, 1, 1, 1, 11, 11, 11, 41, 41, 154, 154, 154, 192, 192, 154, 14, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 38, 39, 40, 41, 42, 23, 24, 25] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 493 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220386 none CC(=O)N(C1=NC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.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, 1, 11, 8, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 1, 1, 1, 1, 1, 8, 8, 43, 43, 43, 42, 42, 63, 87, 87, 43, 43, 43, 1, 1, 6, 14, 14, 16, 16, 16, 8, 8, 43, 43, 43, 63, 63, 43, 1, 14, 14, 14, 14, 14] 201 rigid atoms, others: [3, 4, 5, 6, 7, 21, 22, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 348 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220386 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220386 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220386/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220386 Building REAL300000220387 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220387' /scratch/stefan/7769801/working/building/REAL300000220387 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220387 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220387/0 /scratch/stefan/7769801/working/building/REAL300000220387 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/390 `/scratch/stefan/7769801/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(F)F)C=C2)=N1) `REAL300000220387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220387 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 42, 71, 71, 24, 24, 24, 4, 4, 1, 1, 1, 1, 1, 1, 7, 18, 55, 55, 1, 1, 24, 24, 24, 24, 42, 42, 24, 4, 4, 1, 1, 18, 18, 55, 1, 1] 201 rigid atoms, others: [33, 34, 38, 39, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 452 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220387 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 13, 13, 24, 24, 13, 13, 78, 109, 141, 141, 24, 24, 1, 2, 2, 2, 3, 3, 1, 13, 13, 24, 24, 109, 109, 141, 24, 24] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 525 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220387 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220387 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220387/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220387 Building REAL300000220388 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220388' /scratch/stefan/7769801/working/building/REAL300000220388 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220388 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220388/0 /scratch/stefan/7769801/working/building/REAL300000220388 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/391 `/scratch/stefan/7769801/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1) `REAL300000220388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220388 none CC1=CC(F)=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 10, 10, 62, 62, 62, 61, 61, 90, 106, 106, 62, 62, 62, 1, 10, 10, 10, 10, 10, 10, 1, 1, 10, 10, 62, 62, 62, 90, 90, 62] 201 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 331 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220388 none CC1=CC(F)=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 161, 161, 161, 161, 62, 62, 62, 62, 13, 13, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 61, 161, 161, 161, 161, 161, 161, 62, 62, 13, 13, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 245 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220388 none CC1=CC(F)=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 57, 57, 161, 161, 161, 161, 161, 201, 201, 201, 161, 161, 161, 10, 2, 2, 2, 1, 1, 1, 10, 10, 57, 57, 161, 161, 161, 201, 201, 161] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 506 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220388 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220388 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220388/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220388 Building REAL300000220389 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220389' /scratch/stefan/7769801/working/building/REAL300000220389 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220389 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220389/0 /scratch/stefan/7769801/working/building/REAL300000220389 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/392 `/scratch/stefan/7769801/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CC([N+](=O)[O-])=C3)=N2)=N1) `REAL300000220389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220389 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CC([N+](=O)[O-])=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [74, 73, 74, 74, 108, 120, 120, 74, 74, 74, 12, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 5, 5, 5, 1, 73, 74, 74, 74, 108, 108, 64, 12, 12, 1, 5, 5, 1, 5] 141 rigid atoms, others: [36, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40]) total number of confs: 374 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220389 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CC([N+](=O)[O-])=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 141, 141, 141, 116, 116, 116, 33, 33, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 116, 116, 116, 116, 141, 141, 112, 33, 33, 5, 1, 1, 1, 1] 141 rigid atoms, others: [37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 331 number of broken/clashed sets: 140 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220389 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CC([N+](=O)[O-])=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 74, 74, 74, 74, 116, 116, 74, 116, 116, 116, 116, 116, 74, 1, 2, 2, 2, 3, 3, 1, 11, 11, 74, 116, 116, 74, 116] 141 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 316 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220389 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220389 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220389/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220389 Building REAL300000220390 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220390' /scratch/stefan/7769801/working/building/REAL300000220390 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220390 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220390/0 /scratch/stefan/7769801/working/building/REAL300000220390 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/393 `/scratch/stefan/7769801/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=C(F)C=CC=C3F)O2)=N1) `REAL300000220390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220390 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=C(F)C=CC=C3F)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [67, 66, 67, 67, 99, 103, 103, 67, 67, 67, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 7, 7, 7, 1, 66, 67, 67, 67, 99, 99, 67, 13, 13, 1, 1, 7, 1, 7] 148 rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 319 number of broken/clashed sets: 147 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220390 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=C(F)C=CC=C3F)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 123, 147, 147, 147, 123, 123, 123, 54, 54, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 123, 123, 123, 123, 147, 147, 123, 54, 54, 9, 9, 1, 1, 1] 147 rigid atoms, others: [37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 357 number of broken/clashed sets: 146 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220390 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=C(F)C=CC=C3F)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 67, 123, 123, 123, 67, 123, 123, 123, 67, 1, 2, 2, 2, 3, 3, 1, 12, 12, 67, 67, 123, 67, 123] 148 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 332 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220390 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220390 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220390/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220390 Building REAL300000220391 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220391' /scratch/stefan/7769801/working/building/REAL300000220391 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220391 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220391/0 /scratch/stefan/7769801/working/building/REAL300000220391 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/394 `/scratch/stefan/7769801/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N(C)N=C2C2=CC=CC=C2)N1) `REAL300000220391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220391 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N(C)N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [73, 73, 73, 73, 113, 146, 146, 73, 73, 73, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 73, 73, 73, 73, 113, 113, 11, 11, 2, 2, 2, 7, 7, 2, 7, 7, 73] 151 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 487 number of broken/clashed sets: 150 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220391 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N(C)N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [118, 118, 118, 118, 151, 151, 151, 118, 118, 118, 33, 33, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 151, 151, 33, 33, 7, 7, 7, 1, 1, 1, 1, 1, 118] 151 rigid atoms, others: [37, 38, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 382 number of broken/clashed sets: 150 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220391 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N(C)N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 73, 73, 73, 73, 73, 73, 73, 118, 118, 100, 118, 118, 1, 2, 2, 2, 3, 3, 12, 12, 73, 73, 73, 118, 118, 100, 118, 118, 1] 151 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 26, 42] set([4, 5, 6, 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, 41]) total number of confs: 249 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220391 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220391 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220391/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220391 Building REAL300000220392 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220392' /scratch/stefan/7769801/working/building/REAL300000220392 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220392 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220392/0 /scratch/stefan/7769801/working/building/REAL300000220392 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/395 `/scratch/stefan/7769801/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=N1) `REAL300000220392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220392 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 32, 54, 54, 19, 19, 19, 3, 3, 1, 1, 1, 1, 1, 1, 13, 28, 28, 28, 39, 39, 1, 1, 19, 19, 19, 19, 32, 32, 19, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 303 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220392 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 19, 19, 12, 12, 97, 138, 138, 138, 149, 149, 19, 19, 1, 2, 2, 2, 3, 3, 1, 12, 12, 19, 19, 19, 19] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 460 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220392 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220392 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220392/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220392 Building REAL300000220393 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220393' /scratch/stefan/7769801/working/building/REAL300000220393 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220393 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220393/0 /scratch/stefan/7769801/working/building/REAL300000220393 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/396 `/scratch/stefan/7769801/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)C=C1) `REAL300000220393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220393 none CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 11, 11, 43, 43, 43, 43, 43, 51, 51, 51, 43, 43, 43, 1, 4, 4, 4, 4, 4, 4, 4, 1, 11, 11, 43, 43, 43, 51, 51, 43, 4, 4] 51 rigid atoms, others: [4, 5, 6, 7, 8, 9, 23, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220393 none CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11, 11, 2, 2, 2, 3, 3, 1, 43, 43] 51 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 86 number of broken/clashed sets: 50 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220393 none CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 4, 20, 20, 43, 43, 43, 43, 43, 51, 51, 51, 43, 43, 43, 4, 1, 1, 2, 2, 2, 1, 1, 4, 20, 20, 43, 43, 43, 51, 51, 43, 1, 1] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 41, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 131 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220393 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220393 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220393/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220393 Building REAL300000220394 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220394' /scratch/stefan/7769801/working/building/REAL300000220394 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220394 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220394/0 /scratch/stefan/7769801/working/building/REAL300000220394 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/397 `/scratch/stefan/7769801/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(OC(F)F)=C1) `REAL300000220394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220394 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(OC(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 54, 17, 54, 54, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 54, 54, 108, 146, 146, 54, 91, 91, 91, 54, 54, 11, 11, 2, 2, 2, 3, 3, 1, 146, 54] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 587 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220394 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(OC(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 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: [2, 1, 1, 1, 1, 1, 1, 9, 9, 54, 54, 54, 54, 54, 78, 122, 122, 54, 54, 54, 1, 1, 7, 23, 23, 1, 3, 3, 3, 1, 1, 9, 9, 54, 54, 54, 78, 78, 54, 23, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 20, 21, 25, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 466 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220394 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220394 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220394/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220394 Building REAL300000220395 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220395' /scratch/stefan/7769801/working/building/REAL300000220395 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220395 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220395/0 /scratch/stefan/7769801/working/building/REAL300000220395 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/398 `/scratch/stefan/7769801/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3C=CC(Cl)=CN23)N1) `REAL300000220395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220395 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3C=CC(Cl)=CN23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [39, 39, 39, 39, 56, 56, 56, 39, 39, 39, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 56, 56, 12, 12, 1, 1, 1, 1, 39] 56 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 163 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220395 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3C=CC(Cl)=CN23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 3, 3, 11, 11, 39, 39, 39, 39, 1] 56 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220395 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220395 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220395/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220395 Building REAL300000220396 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220396' /scratch/stefan/7769801/working/building/REAL300000220396 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220396 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220396/0 /scratch/stefan/7769801/working/building/REAL300000220396 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/399 `/scratch/stefan/7769801/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC=CC3=CC=CC=C32)N1) `REAL300000220396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220396 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC=CC3=CC=CC=C32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [41, 41, 41, 41, 52, 52, 52, 41, 41, 41, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 52, 52, 10, 10, 1, 1, 1, 1, 1, 1, 41] 52 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 126 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220396 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC=CC3=CC=CC=C32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 3, 3, 12, 12, 41, 41, 41, 41, 41, 41, 1] 52 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220396 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220396 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220396/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220396 Building REAL300000220397 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220397' /scratch/stefan/7769801/working/building/REAL300000220397 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220397 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220397/0 /scratch/stefan/7769801/working/building/REAL300000220397 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/400 `/scratch/stefan/7769801/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C(C)(C)C)S2)=N1) `REAL300000220397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220397 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C(C)(C)C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 38, 38, 38, 50, 63, 63, 38, 38, 38, 11, 11, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 38, 38, 38, 38, 50, 50, 38, 11, 11, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 63 rigid atoms, others: [12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 208 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220397 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C(C)(C)C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 38, 38, 38, 38, 48, 48, 48, 38, 1, 2, 2, 2, 3, 3, 1, 12, 12, 38, 48, 48, 48, 48, 48, 48, 48, 48, 48] 63 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 144 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220397 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220397 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220397/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220397 Building REAL300000220398 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220398' /scratch/stefan/7769801/working/building/REAL300000220398 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220398 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220398/0 /scratch/stefan/7769801/working/building/REAL300000220398 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/401 `/scratch/stefan/7769801/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1F) `REAL300000220398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220398 none CCN(CC)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [108, 79, 42, 79, 118, 40, 42, 42, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 42, 42, 42, 108, 108, 108, 108, 108, 118, 118, 118, 118, 118, 42, 42, 12, 12, 2, 2, 2, 3, 3, 1, 42] 151 rigid atoms, others: [45, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46]) total number of confs: 598 number of broken/clashed sets: 151 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220398 none CCN(CC)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 4, 1, 4, 14, 1, 1, 1, 1, 1, 5, 5, 42, 42, 42, 42, 42, 74, 109, 109, 42, 42, 42, 1, 1, 1, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 1, 1, 5, 5, 42, 42, 42, 74, 74, 42, 1] 151 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 46, 23, 24, 25, 37] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 470 number of broken/clashed sets: 151 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220398 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220398 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220398/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220398 Building REAL300000220399 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220399' /scratch/stefan/7769801/working/building/REAL300000220399 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220399 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220399/0 /scratch/stefan/7769801/working/building/REAL300000220399 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/402 `/scratch/stefan/7769801/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)N=NN3C)N1) `REAL300000220399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220399 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)N=NN3C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 27, 27, 27, 22, 22, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 27, 27, 7, 7, 1, 1, 1, 2, 2, 2, 22] 27 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 70 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: REAL300000220399 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)N=NN3C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 10, 10, 22, 22, 22, 22, 22, 22, 1] 27 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 63 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220399 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220399 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220399/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220399 Building REAL300000220400 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220400' /scratch/stefan/7769801/working/building/REAL300000220400 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220400 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220400/0 /scratch/stefan/7769801/working/building/REAL300000220400 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/403 `/scratch/stefan/7769801/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2[N+](=O)[O-])=N1) `REAL300000220400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220400 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [31, 31, 31, 31, 41, 41, 41, 31, 31, 31, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 31, 31, 31, 31, 41, 41, 31, 5, 5, 1, 1, 1] 41 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 105 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220400 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 31, 31, 31, 24, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 1, 11, 11, 31, 31, 31] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220400 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220400 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220400/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220400 Building REAL300000220401 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220401' /scratch/stefan/7769801/working/building/REAL300000220401 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220401 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220401/0 /scratch/stefan/7769801/working/building/REAL300000220401 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/404 `/scratch/stefan/7769801/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OC(C)(C)C3)N1) `REAL300000220401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220401 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OC(C)(C)C3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [39, 39, 39, 39, 54, 54, 54, 39, 39, 39, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 54, 54, 12, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 39] 54 rigid atoms, others: [32, 33, 34, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 164 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220401 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OC(C)(C)C3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 3, 3, 10, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1] 54 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 43, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 84 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220401 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220401 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220401/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220401 Building REAL300000220402 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220402' /scratch/stefan/7769801/working/building/REAL300000220402 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220402 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220402/0 /scratch/stefan/7769801/working/building/REAL300000220402 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/405 `/scratch/stefan/7769801/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CN2C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CN=C12) `REAL300000220402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220402 none CC1=CC=CN2C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [33, 33, 33, 33, 33, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 11, 3, 3, 2, 2, 2, 1, 33] 47 rigid atoms, others: [37, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 76 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: REAL300000220402 none CC1=CC=CN2C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 11, 11, 33, 33, 33, 33, 33, 47, 47, 47, 33, 33, 33, 1, 1, 1, 2, 2, 2, 1, 1, 1, 11, 11, 47, 47, 33, 33, 33, 33, 1] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 21, 22, 23, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220402 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220402 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220402/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220402 Building REAL300000220403 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220403' /scratch/stefan/7769801/working/building/REAL300000220403 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220403 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220403/0 /scratch/stefan/7769801/working/building/REAL300000220403 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/406 `/scratch/stefan/7769801/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3C=CC=CN23)N1) `REAL300000220403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220403 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3C=CC=CN23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [31, 31, 31, 31, 47, 47, 47, 31, 31, 31, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 47, 47, 11, 11, 1, 1, 1, 1, 1, 31] 47 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 147 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220403 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3C=CC=CN23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 10, 10, 31, 31, 31, 31, 31, 1] 47 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 78 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220403 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220403 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220403/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220403 Building REAL300000220404 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220404' /scratch/stefan/7769801/working/building/REAL300000220404 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220404 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220404/0 /scratch/stefan/7769801/working/building/REAL300000220404 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/407 `/scratch/stefan/7769801/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C3C=CC(Br)=CN23)=N1) `REAL300000220404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220404 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C3C=CC(Br)=CN23)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 62, 62, 62, 41, 41, 41, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 62, 62, 41, 10, 10, 1, 1, 1, 1] 62 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 185 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220404 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C3C=CC(Br)=CN23)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 3, 3, 1, 11, 11, 41, 41, 41, 41] 62 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 89 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220404 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220404 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220404/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220404 Building REAL300000220405 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220405' /scratch/stefan/7769801/working/building/REAL300000220405 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220405 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220405/0 /scratch/stefan/7769801/working/building/REAL300000220405 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/408 `/scratch/stefan/7769801/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(SC)C=C1OC) `REAL300000220405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220405 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(SC)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 40, 40, 40, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 40, 40, 86, 40, 40, 40, 79, 87, 87, 87, 40, 11, 11, 2, 2, 2, 3, 3, 1, 86, 86, 86, 40, 79, 79, 79] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 307 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220405 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(SC)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 7, 7, 40, 40, 40, 40, 40, 65, 100, 100, 40, 40, 40, 1, 1, 5, 1, 1, 1, 3, 4, 4, 4, 1, 7, 7, 40, 40, 40, 65, 65, 40, 5, 5, 5, 1, 3, 3, 3] 201 rigid atoms, others: [1, 2, 3, 4, 5, 41, 19, 20, 22, 23, 24, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 354 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220405 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220405 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220405/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220405 Building REAL300000220406 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220406' /scratch/stefan/7769801/working/building/REAL300000220406 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220406 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220406/0 /scratch/stefan/7769801/working/building/REAL300000220406 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/409 `/scratch/stefan/7769801/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl) `REAL300000220406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220406 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [39, 24, 22, 24, 24, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 24, 24, 24, 39, 39, 39, 24, 24, 9, 9, 2, 2, 2, 3, 3, 1, 24] 60 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 104 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220406 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 5, 5, 24, 24, 24, 24, 24, 42, 60, 60, 24, 24, 24, 1, 1, 1, 4, 4, 4, 1, 1, 5, 5, 24, 24, 24, 42, 42, 24, 1] 60 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 223 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220406 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220406 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220406/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220406 Building REAL300000220407 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220407' /scratch/stefan/7769801/working/building/REAL300000220407 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220407 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220407/0 /scratch/stefan/7769801/working/building/REAL300000220407 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/410 `/scratch/stefan/7769801/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(C)(C)C)C=C3)O2)=N1) `REAL300000220407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220407 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(C)(C)C)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 67, 68, 68, 99, 139, 139, 68, 68, 68, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 9, 8, 9, 7, 7, 1, 67, 68, 68, 68, 99, 99, 68, 13, 13, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7] 201 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 490 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220407 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(C)(C)C)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 160, 201, 201, 127, 127, 127, 45, 45, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 7, 127, 127, 127, 127, 160, 160, 127, 45, 45, 7, 7, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 201 rigid atoms, others: [51, 39, 40, 50, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 574 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220407 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(C)(C)C)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 68, 68, 68, 68, 127, 127, 68, 68, 145, 145, 145, 127, 127, 68, 1, 2, 2, 2, 3, 3, 1, 12, 12, 68, 68, 127, 127, 145, 145, 145, 146, 145, 145, 145, 145, 145, 127, 127] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 704 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220407 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220407 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220407/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220407 Building REAL300000220408 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220408' /scratch/stefan/7769801/working/building/REAL300000220408 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220408 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220408/0 /scratch/stefan/7769801/working/building/REAL300000220408 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/411 `/scratch/stefan/7769801/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC(F)=CC=C3O2)N1) `REAL300000220408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220408 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC(F)=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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, 25, 25, 37, 37, 37, 25, 25, 25, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 37, 37, 9, 9, 1, 1, 1, 1, 26] 37 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 115 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: REAL300000220408 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC(F)=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 11, 11, 26, 26, 25, 26, 1] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 73 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220408 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220408 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220408/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220408 Building REAL300000220409 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220409' /scratch/stefan/7769801/working/building/REAL300000220409 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220409 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220409/0 /scratch/stefan/7769801/working/building/REAL300000220409 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/412 `/scratch/stefan/7769801/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220409 none COCC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 118, 36, 36, 34, 36, 36, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 36, 163, 163, 163, 118, 118, 34, 36, 36, 10, 10, 3, 3, 2, 2, 2, 1, 36] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 495 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: REAL300000220409 none COCC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 36, 36, 36, 36, 36, 62, 105, 105, 36, 36, 36, 1, 24, 24, 24, 8, 8, 1, 1, 1, 5, 5, 62, 62, 36, 36, 36, 36, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 39, 22, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 426 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220409 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220409 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220409/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220409 Building REAL300000220410 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220410' /scratch/stefan/7769801/working/building/REAL300000220410 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220410 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220410/0 /scratch/stefan/7769801/working/building/REAL300000220410 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/413 `/scratch/stefan/7769801/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2OC(F)F)OCO3)=N1) `REAL300000220410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220410 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2OC(F)F)OCO3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 5, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 92, 150, 150, 59, 59, 59, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 44, 44, 1, 1, 1, 59, 59, 59, 59, 92, 92, 56, 9, 9, 1, 1, 44, 1, 1] 201 rigid atoms, others: [35, 36, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37]) total number of confs: 645 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220410 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2OC(F)F)OCO3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 5, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 59, 59, 59, 59, 59, 59, 131, 185, 185, 59, 59, 59, 1, 2, 2, 2, 3, 3, 1, 12, 12, 59, 59, 185, 59, 59] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 514 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220410 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220410 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220410/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220410 Building REAL300000220411 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220411' /scratch/stefan/7769801/working/building/REAL300000220411 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220411 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220411/0 /scratch/stefan/7769801/working/building/REAL300000220411 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/414 `/scratch/stefan/7769801/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1) `REAL300000220411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220411 none CCC1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 1, 12, 12, 1, 1, 1, 1, 1, 1, 11, 11, 60, 60, 60, 59, 59, 94, 128, 128, 60, 60, 60, 1, 12, 12, 13, 13, 13, 13, 13, 12, 12, 1, 1, 11, 11, 60, 60, 60, 94, 94, 60, 12, 12] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 34, 24] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 488 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220411 none CCC1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 89, 89, 165, 164, 60, 60, 60, 60, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 59, 165, 165, 165, 165, 165, 165, 165, 165, 165, 60, 60, 12, 12, 2, 2, 2, 3, 3, 1, 165, 165] 201 rigid atoms, others: [43, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 765 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220411 none CCC1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 56, 56, 165, 165, 165, 164, 164, 201, 201, 201, 165, 165, 165, 12, 1, 1, 2, 2, 2, 2, 2, 1, 1, 12, 12, 56, 56, 165, 165, 165, 201, 201, 165, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 44, 45, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 493 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220411 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220411 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220411/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220411 Building REAL300000220412 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220412' /scratch/stefan/7769801/working/building/REAL300000220412 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220412 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220412/0 /scratch/stefan/7769801/working/building/REAL300000220412 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/415 `/scratch/stefan/7769801/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OC2CCCC2)=N1) `REAL300000220412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220412 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OC2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 107, 126, 126, 60, 60, 60, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 60, 60, 60, 60, 107, 107, 60, 9, 9, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 465 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220412 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OC2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 125, 201, 201, 201, 125, 125, 125, 42, 42, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 201, 201, 125, 42, 42, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 657 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220412 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OC2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 60, 60, 60, 23, 60, 60, 60, 111, 125, 125, 125, 125, 1, 2, 2, 2, 3, 3, 1, 11, 11, 60, 60, 60, 125, 125, 125, 125, 125, 125, 125, 125, 125] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 356 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220412 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220412 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220412/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220412 Building REAL300000220413 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220413' /scratch/stefan/7769801/working/building/REAL300000220413 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220413 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220413/0 /scratch/stefan/7769801/working/building/REAL300000220413 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/416 `/scratch/stefan/7769801/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CN=CC=N3)C=C2)=N1) `REAL300000220413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220413 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CN=CC=N3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 35, 53, 53, 19, 19, 19, 3, 3, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 23, 1, 1, 19, 19, 19, 19, 35, 35, 19, 3, 3, 1, 1, 23, 23, 23, 1, 1] 201 rigid atoms, others: [35, 36, 40, 41, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 222 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220413 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CN=CC=N3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 201, 201, 201, 130, 130, 130, 42, 42, 23, 20, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 23, 130, 130, 130, 130, 201, 201, 130, 42, 42, 23, 23, 1, 1, 1, 23, 23] 201 rigid atoms, others: [37, 38, 39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 674 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220413 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CN=CC=N3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 19, 19, 9, 17, 77, 130, 130, 130, 130, 130, 19, 19, 1, 2, 2, 2, 3, 3, 1, 9, 9, 19, 19, 130, 130, 130, 19, 19] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 281 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220413 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220413 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220413/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220413 Building REAL300000220414 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220414' /scratch/stefan/7769801/working/building/REAL300000220414 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220414 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220414/0 /scratch/stefan/7769801/working/building/REAL300000220414 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/417 `/scratch/stefan/7769801/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3CCCC3=C2)N1) `REAL300000220414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220414 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3CCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 27, 27, 27, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 27, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19] 27 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 39]) total number of confs: 79 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: REAL300000220414 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3CCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220414 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220414 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220414/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220414 Building REAL300000220415 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220415' /scratch/stefan/7769801/working/building/REAL300000220415 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220415 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220415/0 /scratch/stefan/7769801/working/building/REAL300000220415 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/418 `/scratch/stefan/7769801/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C#N) `REAL300000220415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220415 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [39, 26, 26, 26, 26, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 26, 26, 26, 26, 39, 39, 39, 26, 26, 10, 10, 3, 3, 1, 1, 1, 1, 26] 67 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) 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: REAL300000220415 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 45, 67, 67, 26, 26, 26, 1, 1, 1, 1, 4, 4, 4, 1, 1, 6, 6, 45, 45, 26, 26, 26, 26, 1] 67 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 27, 28, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 249 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220415 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220415 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220415/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220415 Building REAL300000220416 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220416' /scratch/stefan/7769801/working/building/REAL300000220416 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220416 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220416/0 /scratch/stefan/7769801/working/building/REAL300000220416 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/419 `/scratch/stefan/7769801/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220416 none COCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [89, 72, 23, 23, 43, 43, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 43, 43, 89, 89, 89, 72, 72, 43, 43, 12, 12, 3, 3, 2, 2, 2, 1, 43, 43] 108 rigid atoms, others: [37, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 386 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: REAL300000220416 none COCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [18, 5, 1, 1, 1, 1, 1, 1, 6, 6, 43, 43, 43, 43, 43, 65, 85, 85, 43, 43, 43, 1, 1, 18, 18, 18, 5, 5, 1, 1, 6, 6, 65, 65, 43, 43, 43, 43, 1, 1] 108 rigid atoms, others: [2, 3, 4, 5, 6, 7, 39, 21, 22, 38, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 300 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220416 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220416 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220416/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220416 Building REAL300000220417 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220417' /scratch/stefan/7769801/working/building/REAL300000220417 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220417 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220417/0 /scratch/stefan/7769801/working/building/REAL300000220417 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/420 `/scratch/stefan/7769801/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2Br)=N1) `REAL300000220417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220417 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [37, 37, 37, 37, 43, 43, 43, 37, 37, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 43, 43, 37, 7, 7, 1, 1, 1] 43 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 87 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: REAL300000220417 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 37, 37, 37, 28, 37, 37, 37, 1, 2, 2, 2, 3, 3, 1, 11, 11, 37, 37, 37] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220417 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220417 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220417/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220417 Building REAL300000220418 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220418' /scratch/stefan/7769801/working/building/REAL300000220418 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220418 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220418/0 /scratch/stefan/7769801/working/building/REAL300000220418 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/421 `/scratch/stefan/7769801/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=C1) `REAL300000220418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220418 none CC1=C(C)C=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', '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, 1, 12, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 27, 27, 27, 27, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 27, 27, 27, 28, 28, 28, 28, 28, 28, 27, 11, 11, 3, 3, 2, 2, 2, 1, 27, 27] 41 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 83 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: REAL300000220418 none CC1=C(C)C=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', '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, 1, 12, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 27, 27, 41, 41, 41, 27, 28, 27, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 11, 12, 41, 41, 28, 28, 28, 28, 1, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 40, 22, 23, 24, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220418 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220418 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220418/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220418 Building REAL300000220419 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220419' /scratch/stefan/7769801/working/building/REAL300000220419 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220419 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220419/0 /scratch/stefan/7769801/working/building/REAL300000220419 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/422 `/scratch/stefan/7769801/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220419 none CCOC(=O)COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 146, 146, 49, 146, 49, 15, 15, 25, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 25, 25, 157, 157, 157, 157, 157, 49, 49, 25, 25, 8, 8, 2, 2, 2, 3, 3, 1, 25, 25] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 469 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220419 none CCOC(=O)COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 18, 18, 4, 18, 4, 1, 1, 1, 1, 1, 1, 5, 5, 25, 25, 25, 25, 25, 44, 74, 74, 25, 25, 25, 1, 1, 26, 26, 26, 26, 26, 4, 4, 1, 1, 5, 5, 25, 25, 25, 44, 44, 25, 1, 1] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 44, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 347 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220419 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220419 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220419/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220419 Building REAL300000220420 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220420' /scratch/stefan/7769801/working/building/REAL300000220420 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220420 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220420/0 /scratch/stefan/7769801/working/building/REAL300000220420 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/423 `/scratch/stefan/7769801/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(OC(F)F)C=C1C) `REAL300000220420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220420 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(OC(F)F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 15, 15, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 57, 57, 130, 180, 180, 57, 21, 57, 57, 57, 57, 57, 11, 11, 2, 2, 2, 3, 3, 1, 180, 57, 57, 57, 57] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 619 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220420 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(OC(F)F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 15, 15, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 57, 57, 57, 57, 57, 93, 149, 149, 57, 57, 57, 1, 1, 8, 35, 35, 1, 1, 1, 2, 2, 2, 1, 9, 9, 57, 57, 57, 93, 93, 57, 35, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 39, 18, 19, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 626 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220420 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220420 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220420/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220420 Building REAL300000220421 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220421' /scratch/stefan/7769801/working/building/REAL300000220421 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220421 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220421/0 /scratch/stefan/7769801/working/building/REAL300000220421 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/424 `/scratch/stefan/7769801/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2Cl)=N1) `REAL300000220421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220421 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [15, 15, 15, 15, 27, 27, 27, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 27, 27, 15, 7, 7, 1, 1, 1] 27 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 99 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: REAL300000220421 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 15, 15, 9, 15, 15, 15, 15, 1, 2, 2, 2, 3, 3, 1, 9, 9, 15, 15, 15] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 84 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220421 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220421 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220421/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220421 Building REAL300000220422 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220422' /scratch/stefan/7769801/working/building/REAL300000220422 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220422 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220422/0 /scratch/stefan/7769801/working/building/REAL300000220422 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/425 `/scratch/stefan/7769801/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1N1C=NC=N1) `REAL300000220422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220422 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 31, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 31, 31, 16, 27, 68, 68, 68, 68, 31, 31, 31, 31, 11, 11, 3, 3, 1, 1, 1, 1, 31, 31, 68, 68] 98 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 192 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220422 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 9, 9, 2, 8, 26, 26, 68, 68, 68, 68, 68, 98, 98, 98, 68, 68, 68, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 26, 26, 98, 98, 68, 68, 68, 68, 9, 9, 1, 1] 98 rigid atoms, others: [40, 41, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 317 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220422 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 6, 6, 31, 31, 31, 31, 31, 51, 67, 67, 31, 31, 31, 1, 1, 1, 1, 9, 9, 9, 9, 2, 2, 2, 1, 6, 6, 51, 51, 31, 31, 31, 31, 1, 1, 9, 9] 98 rigid atoms, others: [0, 1, 2, 3, 4, 38, 39, 18, 19, 20, 21, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 241 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220422 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220422 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220422/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220422 Building REAL300000220423 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220423' /scratch/stefan/7769801/working/building/REAL300000220423 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220423 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220423/0 /scratch/stefan/7769801/working/building/REAL300000220423 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/426 `/scratch/stefan/7769801/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220423 none COC1=CC=CC=C1C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [11, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 42, 42, 42, 42, 42, 65, 81, 81, 42, 42, 42, 1, 1, 11, 11, 11, 6, 5, 6, 6, 1, 1, 6, 6, 65, 65, 42, 42, 42, 42, 1, 1] 113 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 45, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 285 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220423 none COC1=CC=CC=C1C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [88, 81, 80, 80, 35, 81, 81, 12, 13, 42, 42, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 42, 42, 88, 88, 88, 81, 75, 81, 81, 42, 42, 12, 12, 3, 3, 2, 2, 2, 1, 42, 42] 113 rigid atoms, others: [44, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 368 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220423 none COC1=CC=CC=C1C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 22, 22, 80, 80, 81, 80, 80, 113, 113, 113, 81, 81, 81, 6, 6, 3, 3, 3, 1, 1, 1, 1, 6, 6, 22, 22, 113, 113, 81, 81, 81, 81, 6, 6] 113 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 341 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220423 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220423 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220423/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220423 Building REAL300000220424 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220424' /scratch/stefan/7769801/working/building/REAL300000220424 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220424 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220424/0 /scratch/stefan/7769801/working/building/REAL300000220424 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/427 `/scratch/stefan/7769801/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=CC(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C2)=C1) `REAL300000220424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220424 none CC1=CC(C)=CC(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 13, 19, 24, 24, 13, 13, 13, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 4, 4, 19, 19, 13, 13, 13, 13, 1, 1, 3] 29 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 46, 47, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 48]) total number of confs: 87 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220424 none CC1=CC(C)=CC(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 20, 20, 20, 8, 7, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 12, 12, 20, 20, 20, 20, 12, 20, 20, 20, 20, 12, 12, 7, 7, 3, 3, 2, 2, 2, 1, 12, 12, 20] 29 rigid atoms, others: [45, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 106 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220424 none CC1=CC(C)=CC(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 3, 3, 1, 1, 8, 8, 21, 21, 21, 21, 21, 29, 29, 29, 21, 21, 21, 3, 3, 1, 2, 2, 2, 1, 2, 2, 2, 1, 3, 3, 8, 8, 29, 29, 21, 21, 21, 21, 3, 3, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 48, 35, 27, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220424 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220424 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220424/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220424 Building REAL300000220425 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220425' /scratch/stefan/7769801/working/building/REAL300000220425 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220425 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220425/0 /scratch/stefan/7769801/working/building/REAL300000220425 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/428 `/scratch/stefan/7769801/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CO2)C=C1) `REAL300000220425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220425 none CC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 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: [2, 2, 3, 3, 1, 1, 1, 1, 1, 12, 12, 45, 45, 45, 45, 45, 59, 59, 59, 45, 45, 45, 1, 1, 3, 3, 4, 4, 4, 3, 3, 12, 12, 45, 45, 45, 59, 59, 45, 1, 3, 3] 59 rigid atoms, others: [4, 5, 6, 7, 8, 39, 22, 23] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 171 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220425 none CC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 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: [51, 51, 51, 51, 45, 45, 45, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 45, 45, 51, 51, 51, 51, 51, 51, 51, 10, 10, 2, 2, 2, 3, 3, 1, 45, 51, 51] 59 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220425 none CC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 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, 1, 1, 1, 4, 4, 4, 28, 28, 55, 55, 55, 55, 55, 59, 59, 59, 55, 55, 55, 4, 4, 1, 1, 2, 2, 2, 1, 1, 28, 28, 55, 55, 55, 59, 59, 55, 4, 1, 1] 59 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 41, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220425 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220425 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220425/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220425 Building REAL300000220426 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220426' /scratch/stefan/7769801/working/building/REAL300000220426 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220426 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220426/0 /scratch/stefan/7769801/working/building/REAL300000220426 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/429 `/scratch/stefan/7769801/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220426 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [73, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 44, 44, 73, 73, 73, 44, 11, 11, 3, 3, 2, 2, 2, 1, 44, 44] 89 rigid atoms, others: [39, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 145 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: REAL300000220426 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 44, 44, 44, 44, 44, 65, 89, 89, 44, 44, 44, 1, 1, 4, 4, 4, 1, 9, 9, 65, 65, 44, 44, 44, 44, 1, 1] 89 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 9, 10, 11, 12, 41, 26, 27, 31] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 297 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220426 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220426 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220426/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220426 Building REAL300000220427 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220427' /scratch/stefan/7769801/working/building/REAL300000220427 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220427 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220427/0 /scratch/stefan/7769801/working/building/REAL300000220427 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/430 `/scratch/stefan/7769801/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CSC=C3)S2)=N1) `REAL300000220427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220427 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CSC=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 14, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [47, 47, 47, 47, 57, 57, 57, 47, 47, 47, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 47, 47, 47, 47, 57, 57, 47, 11, 11, 1, 5, 5, 5] 79 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 135 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220427 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CSC=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 14, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [63, 63, 63, 63, 79, 79, 79, 63, 63, 63, 27, 27, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 63, 63, 63, 63, 79, 79, 63, 27, 27, 5, 1, 1, 1] 79 rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 206 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220427 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CSC=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 14, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 47, 47, 47, 47, 63, 63, 63, 63, 47, 1, 2, 2, 2, 3, 3, 1, 9, 9, 47, 63, 63, 63] 79 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 120 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220427 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220427 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220427/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220427 Building REAL300000220428 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220428' /scratch/stefan/7769801/working/building/REAL300000220428 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220428 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220428/0 /scratch/stefan/7769801/working/building/REAL300000220428 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/431 `/scratch/stefan/7769801/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CN=C3)N=C2)N1) `REAL300000220428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220428 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CN=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [21, 21, 21, 21, 27, 27, 27, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 21, 21, 21, 21, 27, 27, 5, 5, 1, 1, 7, 7, 7, 1, 21] 53 rigid atoms, others: [32, 33, 37, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38]) total number of confs: 74 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220428 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CN=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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, 41, 41, 41, 53, 53, 53, 41, 41, 41, 13, 13, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 41, 53, 53, 13, 13, 7, 7, 1, 1, 1, 7, 41] 53 rigid atoms, others: [34, 35, 36, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 132 number of broken/clashed sets: 53 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220428 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CN=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 21, 41, 41, 41, 41, 21, 21, 1, 2, 2, 2, 3, 3, 9, 9, 21, 21, 41, 41, 41, 21, 1] 53 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220428 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220428 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220428/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220428 Building REAL300000220429 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220429' /scratch/stefan/7769801/working/building/REAL300000220429 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220429 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220429/0 /scratch/stefan/7769801/working/building/REAL300000220429 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/432 `/scratch/stefan/7769801/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N1) `REAL300000220429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220429 none COC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 4, 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: [130, 130, 76, 130, 76, 76, 76, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 76, 130, 130, 130, 76, 76, 11, 11, 3, 3, 2, 2, 2, 1, 76] 160 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) 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: REAL300000220429 none COC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 4, 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: [13, 13, 1, 13, 1, 1, 1, 1, 1, 12, 12, 76, 76, 76, 76, 76, 113, 124, 124, 76, 76, 76, 1, 13, 13, 13, 1, 1, 12, 12, 113, 113, 77, 77, 77, 76, 1] 160 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 36, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 396 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220429 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220429 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220429/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220429 Building REAL300000220430 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220430' /scratch/stefan/7769801/working/building/REAL300000220430 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220430 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220430/0 /scratch/stefan/7769801/working/building/REAL300000220430 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/433 `/scratch/stefan/7769801/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CN1) `REAL300000220430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220430 none COC(=O)C1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 40, 88, 40, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 40, 40, 88, 88, 88, 40, 9, 9, 3, 3, 1, 1, 1, 1, 40, 40] 115 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: REAL300000220430 none COC(=O)C1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 4, 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: [12, 12, 1, 12, 1, 1, 1, 1, 6, 6, 40, 40, 40, 40, 40, 64, 89, 89, 40, 40, 40, 1, 1, 13, 13, 13, 1, 6, 6, 64, 64, 40, 40, 40, 40, 1, 1] 115 rigid atoms, others: [2, 35, 4, 5, 6, 7, 21, 22, 36, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220430 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220430 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220430/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220430 Building REAL300000220431 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220431' /scratch/stefan/7769801/working/building/REAL300000220431 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220431 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220431/0 /scratch/stefan/7769801/working/building/REAL300000220431 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/434 `/scratch/stefan/7769801/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1) `REAL300000220431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220431 none CCOC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [153, 123, 115, 48, 115, 48, 48, 48, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 48, 153, 153, 153, 153, 153, 49, 49, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 477 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220431 none CCOC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 17, 9, 1, 9, 1, 1, 1, 1, 1, 10, 10, 48, 48, 48, 48, 48, 83, 116, 116, 48, 49, 48, 1, 24, 24, 24, 24, 24, 1, 1, 10, 10, 49, 49, 49, 83, 83, 48] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 23, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 481 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220431 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220431 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220431/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220431 Building REAL300000220432 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220432' /scratch/stefan/7769801/working/building/REAL300000220432 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220432 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220432/0 /scratch/stefan/7769801/working/building/REAL300000220432 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/435 `/scratch/stefan/7769801/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=C([O-])C(F)=C2)N1) `REAL300000220432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220432 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=C([O-])C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 15, 15, 15, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 15, 15, 4, 4, 1, 1, 8] 15 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 57 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: REAL300000220432 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=C([O-])C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 13, 10, 11, 13, 13, 13, 1, 2, 2, 2, 3, 3, 9, 9, 13, 13, 1] 15 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220432 /scratch/stefan/7769801/working /scratch/stefan/7769801 mkdir: created directory `1' /scratch/stefan/7769801/working/building/REAL300000220432/1 /scratch/stefan/7769801/working/building/REAL300000220432 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 1 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/436 `/scratch/stefan/7769801/working/3D/436' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=C(O)C(F)=C2)N1) `REAL300000220432.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220432/1/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: REAL300000220432 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=C(O)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 15, 15, 15, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 15, 15, 7, 7, 1, 2, 1, 13] 30 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 31, 33]) total number of confs: 38 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: REAL300000220432 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=C(O)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 7, 8, 9, 9, 9, 1, 2, 2, 2, 3, 3, 6, 6, 9, 18, 9, 1] 30 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 70 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220432 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220432 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 1: /scratch/stefan/7769801/working/building/REAL300000220432/1.* 0: /scratch/stefan/7769801/working/building/REAL300000220432/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220432 Building REAL300000220433 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220433' /scratch/stefan/7769801/working/building/REAL300000220433 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220433 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220433/0 /scratch/stefan/7769801/working/building/REAL300000220433 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/437 `/scratch/stefan/7769801/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1OC) `REAL300000220433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220433 none COC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [117, 65, 65, 65, 65, 65, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 65, 65, 65, 123, 117, 117, 117, 65, 65, 65, 65, 12, 12, 3, 3, 2, 2, 2, 1, 65, 123, 123, 123] 161 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 295 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: REAL300000220433 none COC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 65, 65, 65, 65, 65, 103, 133, 133, 65, 65, 65, 1, 1, 1, 3, 4, 4, 4, 1, 2, 2, 2, 9, 9, 103, 103, 65, 65, 65, 64, 1, 4, 4, 4] 161 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 456 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220433 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220433 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220433/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220433 Building REAL300000220434 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220434' /scratch/stefan/7769801/working/building/REAL300000220434 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220434 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220434/0 /scratch/stefan/7769801/working/building/REAL300000220434 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/438 `/scratch/stefan/7769801/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)N=C2)N1) `REAL300000220434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220434 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [20, 20, 20, 20, 25, 25, 25, 20, 20, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 25, 25, 5, 5, 1, 1, 1, 20] 25 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 60 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: REAL300000220434 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 10, 10, 20, 20, 20, 1] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 60 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220434 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220434 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220434/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220434 Building REAL300000220435 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220435' /scratch/stefan/7769801/working/building/REAL300000220435 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220435 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220435/0 /scratch/stefan/7769801/working/building/REAL300000220435 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/439 `/scratch/stefan/7769801/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CS3)S2)=N1) `REAL300000220435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220435 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CS3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 101, 124, 124, 76, 76, 76, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 13, 1, 76, 76, 76, 76, 101, 101, 76, 12, 12, 1, 13, 13, 12] 183 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 360 number of broken/clashed sets: 182 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220435 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CS3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 183, 183, 183, 165, 165, 165, 85, 85, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 13, 165, 165, 165, 165, 183, 183, 165, 85, 84, 13, 1, 1, 1] 183 rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 420 number of broken/clashed sets: 182 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220435 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CS3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 76, 76, 76, 76, 165, 165, 165, 165, 76, 1, 2, 2, 2, 3, 3, 1, 11, 11, 76, 165, 165, 165] 183 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 262 number of broken/clashed sets: 182 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220435 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220435 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220435/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220435 Building REAL300000220436 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220436' /scratch/stefan/7769801/working/building/REAL300000220436 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220436 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220436/0 /scratch/stefan/7769801/working/building/REAL300000220436 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/440 `/scratch/stefan/7769801/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1Br) `REAL300000220436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769801/working/building/REAL300000220436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220436 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 18, 18, 13, 18, 18, 18, 18, 18, 7, 7, 2, 2, 2, 3, 3, 1, 18, 18] 31 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 82 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: REAL300000220436 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 18, 18, 18, 18, 18, 31, 31, 31, 18, 18, 18, 1, 1, 1, 1, 2, 2, 2, 1, 6, 6, 18, 18, 18, 31, 31, 18, 1, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 115 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769801/working/building/REAL300000220436 /scratch/stefan/7769801/working /scratch/stefan/7769801 Finished preparing REAL300000220436 Recording results /scratch/stefan/7769801/working /scratch/stefan/7769801 Appending to /scratch/stefan/7769801/finished/xaaaaim.* 0: /scratch/stefan/7769801/working/building/REAL300000220436/0.* Removing working files in /scratch/stefan/7769801/working/building/REAL300000220436 Building REAL300000220437 mkdir: created directory `/scratch/stefan/7769801/working/building/REAL300000220437' /scratch/stefan/7769801/working/building/REAL300000220437 /scratch/stefan/7769801/working /scratch/stefan/7769801 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220437 mkdir: created directory `0' /scratch/stefan/7769801/working/building/REAL300000220437/0 /scratch/stefan/7769801/working/building/REAL300000220437 /scratch/stefan/7769801/working /scratch/stefan/7769801 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7769801/working/3D/441 `/scratch/stefan/7769801/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C#N)S2)N1) `REAL300000220437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) Error: len(atom_listwat) != numatom: 0 != 31 `/scratch/stefan/7769801/working/building/REAL300000220437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' cp: cannot stat `output.mol2': No such file or directory ls: No match. ls: No match. mv: No match. 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/7769890/working' mkdir: created directory `/scratch/stefan/7769890/working/protonate' Storing results in /scratch/stefan/7769890/finished Working in /scratch/stefan/7769890/working /scratch/stefan/7769890/working /scratch/stefan/7769890 /scratch/stefan/7769890/working/protonate /scratch/stefan/7769890/working /scratch/stefan/7769890 Precomputing protomers for all compounds (pH: 7.4) awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) mv: cannot move `/nfs/home/stefan/.install4j_new' to `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot move `/nfs/home/stefan/.install4j_new' to `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory chmod: cannot access `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: `/nfs/home/stefan/.install4j_new' and `/nfs/home/stefan/.install4j' are the same file mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot move `/nfs/home/stefan/.install4j_new' to `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory ph 7.4: 1037 protomers created Coalesing and merging protomers 1015 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1015 protomers after new stereo-center expansion /scratch/stefan/7769890/working /scratch/stefan/7769890 Bulk generating 3D conformations all protomers in /scratch/stefan/7769890/working/3D mkdir: created directory `/scratch/stefan/7769890/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7769890/working/protonate/xaaaaim-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' 1016 3D conformations generated for 1000 compounds Building REAL300000220001 mkdir: created directory `/scratch/stefan/7769890/working/building' mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220001' /scratch/stefan/7769890/working/building/REAL300000220001 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220001 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220001/0 /scratch/stefan/7769890/working/building/REAL300000220001 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1 `/scratch/stefan/7769890/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1) `REAL300000220001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220001 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 12, 44, 67, 67, 44, 73, 73, 44, 73, 73, 1, 7, 7, 7, 7, 7, 1, 1, 1, 44, 73, 73, 44, 73, 73, 1] 201 rigid atoms, others: [35, 36, 37, 44, 12, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 381 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: REAL300000220001 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 59, 164, 201, 201, 164, 201, 201, 164, 201, 201, 7, 1, 1, 1, 1, 1, 7, 7, 7, 164, 201, 201, 164, 201, 201, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 34, 32, 33, 30, 31] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 852 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220001 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73, 73, 73, 73, 14, 4, 1, 4, 6, 6, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 73, 73, 73, 4, 1, 1, 1, 1, 1, 73] 201 rigid atoms, others: [39, 40, 41, 42, 43, 19, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44]) total number of confs: 471 number of broken/clashed sets: 26 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220001 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220001 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `/scratch/stefan/7769890/finished' Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220001/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220001 Building REAL300000220002 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220002' /scratch/stefan/7769890/working/building/REAL300000220002 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220002 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220002/0 /scratch/stefan/7769890/working/building/REAL300000220002 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/2 `/scratch/stefan/7769890/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C(F)=C3)C(=O)NC2=C1) `REAL300000220002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220002 none N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C(F)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220002 none N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C(F)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220002 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220002 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220002/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220002 Building REAL300000220003 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220003' /scratch/stefan/7769890/working/building/REAL300000220003 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220003 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220003/0 /scratch/stefan/7769890/working/building/REAL300000220003 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/3 `/scratch/stefan/7769890/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C=CC(=O)[O-])O3)C(=O)NC2=C1) `REAL300000220003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220003 none N#CC1=CC=C2C(=CC3=CC=C(C=CC(=O)[O-])O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 9, 9, 11, 11, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 9, 9, 8, 8] 17 rigid atoms, others: [7, 8, 9, 10, 11, 12, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) 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: REAL300000220003 none N#CC1=CC=C2C(=CC3=CC=C(C=CC(=O)[O-])O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 17, 17, 17, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 17, 17, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220003 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220003 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220003/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220003 Building REAL300000220004 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220004' /scratch/stefan/7769890/working/building/REAL300000220004 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220004 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220004/0 /scratch/stefan/7769890/working/building/REAL300000220004 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/4 `/scratch/stefan/7769890/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=C2C(=O)NC3=CC(C#N)=CC=C23)C=C1C(=O)[O-]) `REAL300000220004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220004 none COC1=CC=C(C=C2C(=O)NC3=CC(C#N)=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 7] 13 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 34, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220004 none COC1=CC=C(C=C2C(=O)NC3=CC(C#N)=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 7, 7, 7, 7, 7, 1] 13 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 19, 20, 21, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220004 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220004 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220004/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220004 Building REAL300000220005 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220005' /scratch/stefan/7769890/working/building/REAL300000220005 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220005 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220005/0 /scratch/stefan/7769890/working/building/REAL300000220005 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/5 `/scratch/stefan/7769890/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=CC=C3F)C(=O)NC2=C1) `REAL300000220005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220005 none N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=CC=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4] 4 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 9 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220005 none N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=CC=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28]) total number of confs: 5 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220005 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220005 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220005/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220005 Building REAL300000220006 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220006' /scratch/stefan/7769890/working/building/REAL300000220006 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220006 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220006/0 /scratch/stefan/7769890/working/building/REAL300000220006 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/6 `/scratch/stefan/7769890/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C(=O)[O-])C=C1C=C1C(=O)NC2=CC(C#N)=CC=C12) `REAL300000220006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220006 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 7, 7, 13, 7, 7, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 7, 13, 13, 13, 7, 1, 1, 1, 1, 1] 20 rigid atoms, others: [34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220006 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 1, 3, 3, 3, 1, 7, 7, 7, 7, 7] 20 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 11, 12, 13, 33, 29] set([0, 6, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220006 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220006 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220006/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220006 Building REAL300000220007 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220007' /scratch/stefan/7769890/working/building/REAL300000220007 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220007 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220007/0 /scratch/stefan/7769890/working/building/REAL300000220007 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/7 `/scratch/stefan/7769890/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(F)C(C(=O)[O-])=C3)C(=O)NC2=C1) `REAL300000220007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220007 none N#CC1=CC=C2C(=CC3=CC=C(F)C(C(=O)[O-])=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7] 7 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) 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: REAL300000220007 none N#CC1=CC=C2C(=CC3=CC=C(F)C(C(=O)[O-])=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28]) total number of confs: 8 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220007 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220007 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220007/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220007 Building REAL300000220008 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220008' /scratch/stefan/7769890/working/building/REAL300000220008 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220008 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220008/0 /scratch/stefan/7769890/working/building/REAL300000220008 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/8 `/scratch/stefan/7769890/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=C(CC(=O)[O-])C=C1) `REAL300000220008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220008 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 2, 2, 2, 2, 2, 1, 1, 2, 2, 1, 1] 3 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220008 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 2, 2, 3, 3, 2, 2] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27] set([32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 9 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220008 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220008 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220008/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220008 Building REAL300000220009 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220009' /scratch/stefan/7769890/working/building/REAL300000220009 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220009 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220009/0 /scratch/stefan/7769890/working/building/REAL300000220009 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/9 `/scratch/stefan/7769890/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC(Br)=CC(C(=O)[O-])=C3)C(=O)NC2=C1) `REAL300000220009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220009 none N#CC1=CC=C2C(=CC3=CC(Br)=CC(C(=O)[O-])=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4] 4 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220009 none N#CC1=CC=C2C(=CC3=CC(Br)=CC(C(=O)[O-])=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28]) total number of confs: 5 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220009 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220009 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220009/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220009 Building REAL300000220010 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220010' /scratch/stefan/7769890/working/building/REAL300000220010 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220010 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220010/0 /scratch/stefan/7769890/working/building/REAL300000220010 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/10 `/scratch/stefan/7769890/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C=CC(=O)[O-])C=C3)C(=O)NC2=C1) `REAL300000220010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220010 none N#CC1=CC=C2C(=CC3=CC=C(C=CC(=O)[O-])C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 4, 4, 1, 1, 4, 4] 5 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 17, 18, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34]) total number of confs: 17 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: REAL300000220010 none N#CC1=CC=C2C(=CC3=CC=C(C=CC(=O)[O-])C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 2, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 4, 4, 1, 1] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31]) total number of confs: 17 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220010 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220010 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220010/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220010 Building REAL300000220011 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220011' /scratch/stefan/7769890/working/building/REAL300000220011 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220011 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220011/0 /scratch/stefan/7769890/working/building/REAL300000220011 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/11 `/scratch/stefan/7769890/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC(F)=C(C(=O)[O-])C=C3F)C(=O)NC2=C1) `REAL300000220011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220011 none N#CC1=CC=C2C(=CC3=CC(F)=C(C(=O)[O-])C=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220011 none N#CC1=CC=C2C(=CC3=CC(F)=C(C(=O)[O-])C=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220011 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220011 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220011/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220011 Building REAL300000220012 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220012' /scratch/stefan/7769890/working/building/REAL300000220012 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220012 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220012/0 /scratch/stefan/7769890/working/building/REAL300000220012 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/12 `/scratch/stefan/7769890/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=C2C(=CC=C1)NN=C2C(=O)[O-]) `REAL300000220012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220012 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=C2C(=CC=C1)NN=C2C(=O)[O-] NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 1, 1, 1, 1] 5 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220012 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=C2C(=CC=C1)NN=C2C(=O)[O-] NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29] set([32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 6 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220012 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220012 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220012/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220012 Building REAL300000220013 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220013' /scratch/stefan/7769890/working/building/REAL300000220013 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220013 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220013/0 /scratch/stefan/7769890/working/building/REAL300000220013 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/13 `/scratch/stefan/7769890/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)C(=O)NC2=C1) `REAL300000220013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220013 none N#CC1=CC=C2C(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 11, 11, 1, 1, 1, 6, 6, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 6, 6, 3, 6, 6, 7, 7] 33 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 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: REAL300000220013 none N#CC1=CC=C2C(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 7, 7, 7, 26, 28, 28, 7, 7, 7, 20, 20, 8, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 7, 26, 26, 20, 20, 11, 20, 20, 1, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 23, 24, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: REAL300000220013 none N#CC1=CC=C2C(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 20, 20, 20, 6, 6, 6, 6, 6, 21, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 6, 21, 21, 1, 1, 1, 1, 1, 20, 20] 33 rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 115 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220013 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220013 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220013/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220013 Building REAL300000220014 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220014' /scratch/stefan/7769890/working/building/REAL300000220014 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220014 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220014/0 /scratch/stefan/7769890/working/building/REAL300000220014 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/14 `/scratch/stefan/7769890/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)C(=O)NC2=C1) `REAL300000220014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220014 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 19, 19, 11, 11, 11, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 11, 11, 22, 11, 9, 9] 80 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) 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: REAL300000220014 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 40, 40, 80, 40, 1, 1] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 23, 24, 25, 26, 27, 28, 29, 30, 37] set([32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31]) 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: REAL300000220014 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [40, 40, 40, 40, 40, 40, 40, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 40, 40, 40, 40, 40, 40, 40, 40, 11, 11, 1, 1, 2, 1, 40, 40] 80 rigid atoms, others: [33, 34, 36, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 37, 38]) total number of confs: 96 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220014 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220014 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220014/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220014 Building REAL300000220015 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220015' /scratch/stefan/7769890/working/building/REAL300000220015 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220015 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220015/0 /scratch/stefan/7769890/working/building/REAL300000220015 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/15 `/scratch/stefan/7769890/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)C(=O)NC2=C1) `REAL300000220015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220015 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 2, 3, 3, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1, 3, 3] 3 rigid atoms, others: [32, 37, 38, 7, 8, 9, 10, 11, 12, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39, 40]) total number of confs: 15 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: REAL300000220015 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 23, 24, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 9 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: REAL300000220015 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3] 3 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 18 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220015 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220015 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220015/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220015 Building REAL300000220016 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220016' /scratch/stefan/7769890/working/building/REAL300000220016 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220016 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220016/0 /scratch/stefan/7769890/working/building/REAL300000220016 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/16 `/scratch/stefan/7769890/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CNC4=CC=C(C(=O)[O-])C=C34)C(=O)NC2=C1) `REAL300000220016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220016 none N#CC1=CC=C2C(=CC3=CNC4=CC=C(C(=O)[O-])C=C34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4] 4 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 34, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 9 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220016 none N#CC1=CC=C2C(=CC3=CNC4=CC=C(C(=O)[O-])C=C34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 20, 21, 22, 23, 24, 25, 26, 27] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31]) total number of confs: 5 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220016 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220016 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220016/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220016 Building REAL300000220017 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220017' /scratch/stefan/7769890/working/building/REAL300000220017 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220017 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220017/0 /scratch/stefan/7769890/working/building/REAL300000220017 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/17 `/scratch/stefan/7769890/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C32)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000220017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220017 none COC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C32)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [18, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 24, 47, 47, 48, 48, 18, 18, 18, 7, 1, 1, 1, 1, 1, 7, 47, 47, 47, 47] 48 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 36] set([0, 1, 2, 3, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41]) 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: REAL300000220017 none COC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C32)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 18, 18, 26, 26, 3, 3, 3, 1, 7, 7, 7, 7, 7, 1, 18, 18, 18, 18] 48 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 37, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220017 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220017 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220017/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220017 Building REAL300000220018 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220018' /scratch/stefan/7769890/working/building/REAL300000220018 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220018 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220018/0 /scratch/stefan/7769890/working/building/REAL300000220018 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/18 `/scratch/stefan/7769890/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C(O)=C3)C(=O)NC2=C1) `REAL300000220018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220018 none N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C(O)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 1, 3, 3] 6 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 26, 27, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 28, 30, 31]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220018 none N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C(O)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 3, 1, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220018 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220018 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220018/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220018 Building REAL300000220019 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220019' /scratch/stefan/7769890/working/building/REAL300000220019 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220019 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220019/0 /scratch/stefan/7769890/working/building/REAL300000220019 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/19 `/scratch/stefan/7769890/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=C2C(=O)NC3=CC(C#N)=CC=C23)C=C1C(=O)[O-]) `REAL300000220019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220019 none CC1=CC=C(C=C2C(=O)NC3=CC(C#N)=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7] 7 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 33, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220019 none CC1=CC=C(C=C2C(=O)NC3=CC(C#N)=CC=C23)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 18, 19, 20, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220019 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220019 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220019/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220019 Building REAL300000220020 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220020' /scratch/stefan/7769890/working/building/REAL300000220020 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220020 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220020/0 /scratch/stefan/7769890/working/building/REAL300000220020 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/20 `/scratch/stefan/7769890/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=C(Cl)S3)C(=O)NC2=C1) `REAL300000220020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220020 none N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=C(Cl)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7] 7 rigid atoms, others: [7, 8, 9, 10, 11, 14, 15, 16, 25] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27]) 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: REAL300000220020 none N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=C(Cl)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 1, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 25]) total number of confs: 8 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220020 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220020 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220020/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220020 Building REAL300000220021 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220021' /scratch/stefan/7769890/working/building/REAL300000220021 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220021 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220021/0 /scratch/stefan/7769890/working/building/REAL300000220021 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/21 `/scratch/stefan/7769890/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)C(=O)NC2=C1) `REAL300000220021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220021 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 2, 3, 5, 5, 5, 5, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 5, 5, 5, 5, 4, 4] 9 rigid atoms, others: [7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) 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: REAL300000220021 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 9, 4, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 1, 1] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 37, 22, 23, 24, 25, 26, 27, 28, 29, 36] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220021 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 1, 1, 1, 1, 9, 9] 9 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 24 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220021 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220021 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220021/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220021 Building REAL300000220022 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220022' /scratch/stefan/7769890/working/building/REAL300000220022 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220022 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220022/0 /scratch/stefan/7769890/working/building/REAL300000220022 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/22 `/scratch/stefan/7769890/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)C(=O)NC2=C1) `REAL300000220022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220022 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 6, 4, 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: [8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 11, 11, 22, 11, 8, 8] 54 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220022 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 27, 54, 27, 1, 1] 54 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 23, 24, 25, 26, 27, 28, 29, 30, 37] set([32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220022 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 6, 4, 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: [27, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 1, 1, 2, 1, 27, 27] 54 rigid atoms, others: [33, 34, 36, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 37, 38]) total number of confs: 66 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220022 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220022 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220022/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220022 Building REAL300000220023 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220023' /scratch/stefan/7769890/working/building/REAL300000220023 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220023 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220023/0 /scratch/stefan/7769890/working/building/REAL300000220023 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/23 `/scratch/stefan/7769890/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)C(=O)NC2=C1) `REAL300000220023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220023 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 11, 11, 11, 11, 7, 7] 19 rigid atoms, others: [7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 26 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220023 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 37, 22, 23, 24, 25, 26, 27, 28, 29, 36] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220023 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 1, 1, 1, 1, 19, 19] 19 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 44 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220023 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220023 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220023/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220023 Building REAL300000220024 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220024' /scratch/stefan/7769890/working/building/REAL300000220024 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220024 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220024/0 /scratch/stefan/7769890/working/building/REAL300000220024 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/24 `/scratch/stefan/7769890/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=C1C(=O)NC2=CC(C#N)=CC=C12) `REAL300000220024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220024 none COC1=CC=C(C(=O)[O-])C=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1] 5 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28, 29]) total number of confs: 6 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220024 none COC1=CC=C(C(=O)[O-])C=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5] 5 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 27, 28, 29] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220024 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220024 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220024/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220024 Building REAL300000220025 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220025' /scratch/stefan/7769890/working/building/REAL300000220025 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220025 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220025/0 /scratch/stefan/7769890/working/building/REAL300000220025 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/25 `/scratch/stefan/7769890/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CSC4=CC=C(C(=O)[O-])C=C34)C(=O)NC2=C1) `REAL300000220025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220025 none N#CC1=CC=C2C(=CC3=CSC4=CC=C(C(=O)[O-])C=C34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220025 none N#CC1=CC=C2C(=CC3=CSC4=CC=C(C(=O)[O-])C=C34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220025 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220025 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220025/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220025 Building REAL300000220026 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220026' /scratch/stefan/7769890/working/building/REAL300000220026 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220026 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220026/0 /scratch/stefan/7769890/working/building/REAL300000220026 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/26 `/scratch/stefan/7769890/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=CC=C3Br)C(=O)NC2=C1) `REAL300000220026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220026 none N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=CC=C3Br)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220026 none N#CC1=CC=C2C(=CC3=CC(C(=O)[O-])=CC=C3Br)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220026 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220026 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220026/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220026 Building REAL300000220027 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220027' /scratch/stefan/7769890/working/building/REAL300000220027 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220027 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220027/0 /scratch/stefan/7769890/working/building/REAL300000220027 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/27 `/scratch/stefan/7769890/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C=C3[N+](=O)[O-])C(=O)NC2=C1) `REAL300000220027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220027 none N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C=C3[N+](=O)[O-])C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220027 none N#CC1=CC=C2C(=CC3=CC=C(C(=O)[O-])C=C3[N+](=O)[O-])C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 25, 26, 27, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220027 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220027 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220027/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220027 Building REAL300000220028 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220028' /scratch/stefan/7769890/working/building/REAL300000220028 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220028 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220028/0 /scratch/stefan/7769890/working/building/REAL300000220028 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/28 `/scratch/stefan/7769890/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=CC(CC(=O)[O-])=C1) `REAL300000220028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220028 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=CC(CC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 4, 4, 4, 4, 4, 1, 1, 1, 3, 3, 1] 6 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18, 22, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32]) total number of confs: 18 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220028 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=CC(CC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 4, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 4] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27] set([32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220028 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220028 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220028/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220028 Building REAL300000220029 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220029' /scratch/stefan/7769890/working/building/REAL300000220029 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220029 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220029/0 /scratch/stefan/7769890/working/building/REAL300000220029 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/29 `/scratch/stefan/7769890/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C23)=CC=C1C(=O)[O-]) `REAL300000220029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220029 none COC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C23)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 5, 5] 7 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 33, 34, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 18 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220029 none COC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C23)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 5, 5, 5, 5, 5, 1, 1] 7 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 18, 19, 20, 21, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220029 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220029 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220029/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220029 Building REAL300000220030 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220030' /scratch/stefan/7769890/working/building/REAL300000220030 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220030 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220030/0 /scratch/stefan/7769890/working/building/REAL300000220030 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/30 `/scratch/stefan/7769890/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=C(F)C=C(C(=O)[O-])C=C3F)C(=O)NC2=C1) `REAL300000220030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220030 none N#CC1=CC=C2C(=CC3=C(F)C=C(C(=O)[O-])C=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2] 2 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 9 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220030 none N#CC1=CC=C2C(=CC3=C(F)C=C(C(=O)[O-])C=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1] 2 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220030 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220030 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220030/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220030 Building REAL300000220031 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220031' /scratch/stefan/7769890/working/building/REAL300000220031 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220031 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220031/0 /scratch/stefan/7769890/working/building/REAL300000220031 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/31 `/scratch/stefan/7769890/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=C(F)C=CC(C(=O)[O-])=C3F)C(=O)NC2=C1) `REAL300000220031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220031 none N#CC1=CC=C2C(=CC3=C(F)C=CC(C(=O)[O-])=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 7, 7] 7 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) 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: REAL300000220031 none N#CC1=CC=C2C(=CC3=C(F)C=CC(C(=O)[O-])=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28]) total number of confs: 8 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220031 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220031 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220031/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220031 Building REAL300000220032 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220032' /scratch/stefan/7769890/working/building/REAL300000220032 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220032 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220032/0 /scratch/stefan/7769890/working/building/REAL300000220032 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/32 `/scratch/stefan/7769890/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1) `REAL300000220032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220032 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 5, 1, 1, 2, 2, 2, 2, 2, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1] 9 rigid atoms, others: [34, 35, 42, 43, 12, 13, 14, 15, 16, 17, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220032 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 5, 5, 9, 9, 9, 5, 2, 2, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 9, 9, 5, 2, 2] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 33, 29, 30, 31] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) 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: REAL300000220032 none N#CC1=CC=C2C(=C1)NC(=O)C2=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 5, 5, 5, 5, 5, 5, 3, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 3, 1, 5, 5] 9 rigid atoms, others: [36, 37, 38, 41, 16, 17, 18, 19, 20, 21, 22, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 42, 43]) total number of confs: 30 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220032 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220032 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220032/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220032 Building REAL300000220033 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220033' /scratch/stefan/7769890/working/building/REAL300000220033 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220033 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220033/0 /scratch/stefan/7769890/working/building/REAL300000220033 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/33 `/scratch/stefan/7769890/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C23)=CC=C1OCC(=O)[O-]) `REAL300000220033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220033 none CCOC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C23)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 36, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 53, 143, 167, 167, 109, 109, 109, 109, 109, 7, 1, 1, 1, 1, 1, 7, 7, 143, 143] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 37] set([0, 1, 2, 3, 4, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41]) total number of confs: 870 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: REAL300000220033 none CCOC1=CC(C=C2C(=O)NC3=CC(C#N)=CC=C23)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 9, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 9, 47, 88, 88, 41, 41, 41, 41, 41, 1, 7, 7, 7, 7, 7, 1, 1, 47, 47] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 19, 20, 21, 22, 38] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 423 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220033 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220033 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220033/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220033 Building REAL300000220034 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220034' /scratch/stefan/7769890/working/building/REAL300000220034 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220034 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220034/0 /scratch/stefan/7769890/working/building/REAL300000220034 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/34 `/scratch/stefan/7769890/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC(F)=C(C(=O)[O-])C(F)=C3)C(=O)NC2=C1) `REAL300000220034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220034 none N#CC1=CC=C2C(=CC3=CC(F)=C(C(=O)[O-])C(F)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2] 2 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 9 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220034 none N#CC1=CC=C2C(=CC3=CC(F)=C(C(=O)[O-])C(F)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1] 2 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28]) total number of confs: 3 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220034 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220034 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220034/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220034 Building REAL300000220035 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220035' /scratch/stefan/7769890/working/building/REAL300000220035 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220035 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220035/0 /scratch/stefan/7769890/working/building/REAL300000220035 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/35 `/scratch/stefan/7769890/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC4=C(C=C(C(=O)[O-])N4)O3)C(=O)NC2=C1) `REAL300000220035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220035 none N#CC1=CC=C2C(=CC3=CC4=C(C=C(C(=O)[O-])N4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5] 5 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220035 none N#CC1=CC=C2C(=CC3=CC4=C(C=C(C(=O)[O-])N4)O3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29]) total number of confs: 6 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220035 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220035 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220035/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220035 Building REAL300000220036 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220036' /scratch/stefan/7769890/working/building/REAL300000220036 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220036 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220036/0 /scratch/stefan/7769890/working/building/REAL300000220036 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/36 `/scratch/stefan/7769890/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C4OC(C(=O)[O-])=CC4=C3)C(=O)NC2=C1) `REAL300000220036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220036 none N#CC1=CC=C2C(=CC3=CC=C4OC(C(=O)[O-])=CC4=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 15, 16, 33, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220036 none N#CC1=CC=C2C(=CC3=CC=C4OC(C(=O)[O-])=CC4=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220036 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220036 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220036/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220036 Building REAL300000220037 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220037' /scratch/stefan/7769890/working/building/REAL300000220037 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220037 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220037/0 /scratch/stefan/7769890/working/building/REAL300000220037 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/37 `/scratch/stefan/7769890/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=CN4C(C(=O)[O-])=CN=C34)C(=O)NC2=C1) `REAL300000220037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220037 none N#CC1=CC=C2C(=CC3=CC=CN4C(C(=O)[O-])=CN=C34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 15, 16, 33, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220037 none N#CC1=CC=C2C(=CC3=CC=CN4C(C(=O)[O-])=CN=C34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220037 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220037 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220037/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220037 Building REAL300000220038 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220038' /scratch/stefan/7769890/working/building/REAL300000220038 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220038 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220038/0 /scratch/stefan/7769890/working/building/REAL300000220038 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/38 `/scratch/stefan/7769890/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=C1C(=O)NC2=CC(C#N)=CC=C12) `REAL300000220038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220038 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 3 rigid atoms, others: [34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220038 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220038 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220038 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220038/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220038 Building REAL300000220039 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220039' /scratch/stefan/7769890/working/building/REAL300000220039 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220039 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220039/0 /scratch/stefan/7769890/working/building/REAL300000220039 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/39 `/scratch/stefan/7769890/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CN=C4C=CC(C(=O)[O-])=CN34)C(=O)NC2=C1) `REAL300000220039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220039 none N#CC1=CC=C2C(=CC3=CN=C4C=CC(C(=O)[O-])=CN34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4] 4 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 33, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220039 none N#CC1=CC=C2C(=CC3=CN=C4C=CC(C(=O)[O-])=CN34)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31]) total number of confs: 5 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220039 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220039 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220039/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220039 Building REAL300000220040 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220040' /scratch/stefan/7769890/working/building/REAL300000220040 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220040 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220040/0 /scratch/stefan/7769890/working/building/REAL300000220040 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/40 `/scratch/stefan/7769890/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)C(=O)NC2=C1) `REAL300000220040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220040 none N#CC1=CC=C2C(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 7, 7, 1, 1, 4, 4] 7 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 36, 37]) total number of confs: 16 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220040 none N#CC1=CC=C2C(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 4, 4, 1, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 37, 22, 23, 24, 25, 26, 27, 28, 29, 36] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220040 none N#CC1=CC=C2C(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 7, 7, 7, 7] 7 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 30 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220040 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220040 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220040/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220040 Building REAL300000220041 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220041' /scratch/stefan/7769890/working/building/REAL300000220041 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220041 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220041/0 /scratch/stefan/7769890/working/building/REAL300000220041 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/41 `/scratch/stefan/7769890/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=CC(C(=O)[O-])=C3F)C(=O)NC2=C1) `REAL300000220041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220041 none N#CC1=CC=C2C(=CC3=CC=CC(C(=O)[O-])=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7] 7 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) 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: REAL300000220041 none N#CC1=CC=C2C(=CC3=CC=CC(C(=O)[O-])=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28]) total number of confs: 8 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220041 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220041 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220041/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220041 Building REAL300000220042 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220042' /scratch/stefan/7769890/working/building/REAL300000220042 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220042 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220042/0 /scratch/stefan/7769890/working/building/REAL300000220042 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/42 `/scratch/stefan/7769890/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(OCC(=O)[O-])C(Cl)=C3)C(=O)NC2=C1) `REAL300000220042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220042 none N#CC1=CC=C2C(=CC3=CC=C(OCC(=O)[O-])C(Cl)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 36, 42, 42, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 36, 36, 1, 7, 7] 49 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 33, 34]) total number of confs: 154 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: REAL300000220042 none N#CC1=CC=C2C(=CC3=CC=C(OCC(=O)[O-])C(Cl)=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 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, 1, 1, 1, 1, 1, 1, 7, 7, 4, 7, 28, 49, 49, 49, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 49, 49, 7, 1, 1] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 20, 21, 22, 23, 24, 25, 26, 27] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31]) total number of confs: 155 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220042 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220042 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220042/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220042 Building REAL300000220043 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220043' /scratch/stefan/7769890/working/building/REAL300000220043 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220043 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220043/0 /scratch/stefan/7769890/working/building/REAL300000220043 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/43 `/scratch/stefan/7769890/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(S(=O)(=O)NCC(=O)[O-])C=C3)C(=O)NC2=C1) `REAL300000220043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220043 none N#CC1=CC=C2C(=CC3=CC=C(S(=O)(=O)NCC(=O)[O-])C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 32, 34, 34, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 9, 32, 32, 1, 1, 4, 4] 35 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38]) 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: REAL300000220043 none N#CC1=CC=C2C(=CC3=CC=C(S(=O)(=O)NCC(=O)[O-])C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 20, 35, 35, 35, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 20, 35, 35, 4, 4, 1, 1] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 22, 23, 24, 25, 26, 27, 28, 29, 37] set([32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220043 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220043 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220043/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220043 Building REAL300000220044 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220044' /scratch/stefan/7769890/working/building/REAL300000220044 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220044 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220044/0 /scratch/stefan/7769890/working/building/REAL300000220044 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/44 `/scratch/stefan/7769890/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)C(=O)NC2=C1) `REAL300000220044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220044 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 8, 8, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 7, 7, 6, 7, 1, 1, 4, 4] 8 rigid atoms, others: [32, 37, 38, 7, 8, 9, 10, 11, 12, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39, 40]) 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: REAL300000220044 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 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, 1, 1, 1, 4, 4, 1, 1, 8, 8, 7, 8, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 4, 4, 1, 1] 8 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 39, 23, 24, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220044 none N#CC1=CC=C2C(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 1, 1, 1, 1, 7, 7, 8, 8] 8 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 38 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220044 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220044 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220044/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220044 Building REAL300000220045 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220045' /scratch/stefan/7769890/working/building/REAL300000220045 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220045 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220045/0 /scratch/stefan/7769890/working/building/REAL300000220045 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/45 `/scratch/stefan/7769890/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=C1C(=O)NC2=CC(C#N)=CC=C12) `REAL300000220045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220045 none COC1=CC(C(=O)[O-])=CC=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1] 5 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28, 29]) total number of confs: 6 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220045 none COC1=CC(C(=O)[O-])=CC=C1C=C1C(=O)NC2=CC(C#N)=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 1, 1, 1, 5, 5, 5, 5, 5] 5 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 27, 28, 29] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 18 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220045 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220045 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220045/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220045 Building REAL300000220046 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220046' /scratch/stefan/7769890/working/building/REAL300000220046 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220046 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220046/0 /scratch/stefan/7769890/working/building/REAL300000220046 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/46 `/scratch/stefan/7769890/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2C(=CC3=C4C=C(C(=O)[O-])SC4=CC=C3F)C(=O)NC2=C1) `REAL300000220046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220046 none N#CC1=CC=C2C(=CC3=C4C=C(C(=O)[O-])SC4=CC=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 33, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220046 none N#CC1=CC=C2C(=CC3=C4C=C(C(=O)[O-])SC4=CC=C3F)C(=O)NC2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 21, 22, 23, 24, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220046 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220046 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220046/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220046 Building REAL300000220047 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220047' /scratch/stefan/7769890/working/building/REAL300000220047 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220047 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220047/0 /scratch/stefan/7769890/working/building/REAL300000220047 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/47 `/scratch/stefan/7769890/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C(F)=C2)N1) `REAL300000220047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220047 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [25, 25, 25, 25, 38, 42, 42, 25, 25, 25, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 25, 25, 25, 25, 38, 38, 5, 5, 1, 1, 5, 5, 1, 25] 56 rigid atoms, others: [33, 34, 37, 12, 13, 14, 15, 16, 17, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 38]) total number of confs: 134 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220047 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 25, 42, 42, 42, 42, 25, 25, 25, 1, 2, 2, 2, 3, 3, 11, 11, 25, 25, 42, 42, 25, 1] 56 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 25] set([4, 5, 6, 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: 99 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220047 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [42, 42, 42, 42, 56, 56, 56, 42, 42, 42, 14, 14, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 42, 42, 42, 42, 56, 56, 14, 14, 5, 5, 1, 1, 5, 42] 56 rigid atoms, others: [35, 36, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 167 number of broken/clashed sets: 56 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220047 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220047 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220047/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220047 Building REAL300000220048 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220048' /scratch/stefan/7769890/working/building/REAL300000220048 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220048 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220048/0 /scratch/stefan/7769890/working/building/REAL300000220048 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/48 `/scratch/stefan/7769890/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=C(Cl)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220048 none CCCOC1=C(Cl)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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, 12, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 79, 59, 31, 31, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 31, 31, 31, 71, 138, 138, 138, 138, 138, 79, 79, 31, 9, 9, 2, 2, 2, 3, 3, 1, 31, 71, 71, 71] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 647 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220048 none CCCOC1=C(Cl)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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, 12, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 31, 31, 31, 31, 31, 58, 101, 101, 31, 31, 31, 1, 1, 1, 3, 15, 15, 15, 14, 14, 8, 8, 1, 5, 5, 31, 31, 31, 58, 58, 31, 1, 4, 4, 4] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 43, 23, 24, 25] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 456 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220048 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220048 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220048/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220048 Building REAL300000220049 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220049' /scratch/stefan/7769890/working/building/REAL300000220049 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220049 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220049/0 /scratch/stefan/7769890/working/building/REAL300000220049 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/49 `/scratch/stefan/7769890/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)O2)N1) `REAL300000220049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220049 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 75, 87, 87, 51, 52, 51, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 12, 1, 52, 52, 52, 52, 75, 75, 12, 12, 1, 1, 12, 12, 10, 12, 52] 201 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 300 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220049 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 52, 52, 52, 52, 165, 165, 72, 165, 165, 165, 52, 1, 2, 2, 2, 3, 3, 11, 11, 52, 52, 165, 165, 165, 165, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 39] set([4, 5, 6, 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: 553 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220049 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 201, 201, 201, 165, 165, 165, 67, 67, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 165, 165, 165, 165, 201, 201, 67, 67, 12, 12, 1, 1, 1, 1, 165] 201 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 505 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220049 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220049 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220049/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220049 Building REAL300000220050 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220050' /scratch/stefan/7769890/working/building/REAL300000220050 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220050 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220050/0 /scratch/stefan/7769890/working/building/REAL300000220050 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/50 `/scratch/stefan/7769890/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC(F)F) `REAL300000220050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220050 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 31, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 31, 31, 31, 94, 145, 145, 85, 85, 85, 31, 31, 9, 9, 2, 2, 2, 3, 3, 1, 31, 145] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 534 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220050 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 31, 31, 31, 31, 31, 57, 95, 95, 31, 31, 31, 1, 1, 1, 7, 15, 15, 4, 4, 4, 1, 1, 5, 5, 31, 31, 31, 57, 57, 31, 1, 15] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 20, 21, 22, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 401 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220050 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220050 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220050/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220050 Building REAL300000220051 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220051' /scratch/stefan/7769890/working/building/REAL300000220051 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220051 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220051/0 /scratch/stefan/7769890/working/building/REAL300000220051 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/51 `/scratch/stefan/7769890/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(Cl)C=C3)=N2)=N1) `REAL300000220051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220051 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(Cl)C=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [45, 44, 45, 45, 68, 68, 68, 45, 45, 45, 12, 12, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 3, 1, 44, 45, 45, 45, 68, 68, 41, 12, 12, 1, 3, 3, 3, 3] 68 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 220 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220051 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(Cl)C=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 45, 45, 45, 45, 54, 54, 53, 54, 54, 54, 45, 1, 2, 2, 2, 3, 3, 1, 11, 11, 45, 54, 54, 54, 54] 68 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 114 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220051 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(Cl)C=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [54, 54, 54, 54, 68, 68, 68, 54, 54, 54, 23, 23, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 54, 54, 54, 54, 68, 68, 53, 23, 23, 3, 1, 1, 1, 1] 68 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 179 number of broken/clashed sets: 67 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220051 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220051 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220051/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220051 Building REAL300000220052 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220052' /scratch/stefan/7769890/working/building/REAL300000220052 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220052 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220052/0 /scratch/stefan/7769890/working/building/REAL300000220052 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/52 `/scratch/stefan/7769890/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)=C1) `REAL300000220052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220052 none COC1=CC=CC(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 12, 12, 63, 63, 64, 64, 64, 98, 141, 141, 64, 64, 64, 1, 1, 4, 9, 9, 9, 4, 4, 4, 12, 12, 64, 64, 64, 98, 98, 60, 1, 4] 201 rigid atoms, others: [6, 7, 8, 9, 10, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 483 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220052 none COC1=CC=CC(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 37, 37, 133, 133, 133, 133, 133, 171, 201, 201, 133, 133, 133, 4, 4, 1, 3, 3, 3, 1, 1, 1, 37, 37, 133, 133, 133, 171, 171, 130, 4, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 42, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 552 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220052 none COC1=CC=CC(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 133, 133, 133, 133, 133, 64, 64, 64, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 64, 64, 133, 163, 163, 163, 133, 133, 133, 12, 12, 2, 2, 2, 3, 3, 1, 64, 133] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 278 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220052 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220052 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220052/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220052 Building REAL300000220053 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220053' /scratch/stefan/7769890/working/building/REAL300000220053 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220053 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220053/0 /scratch/stefan/7769890/working/building/REAL300000220053 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/53 `/scratch/stefan/7769890/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC(F)F) `REAL300000220053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220053 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 67, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 27, 27, 27, 27, 113, 166, 166, 68, 68, 68, 68, 68, 27, 9, 9, 2, 2, 2, 3, 3, 1, 27, 27, 166] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 530 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220053 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 5, 1, 1, 1, 1, 1, 5, 5, 27, 27, 27, 27, 27, 48, 83, 83, 27, 27, 27, 1, 1, 1, 1, 9, 25, 25, 6, 6, 6, 6, 6, 1, 5, 5, 27, 27, 27, 48, 48, 27, 1, 1, 25] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 41, 42, 20, 21, 22, 23] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 387 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220053 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220053 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220053/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220053 Building REAL300000220054 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220054' /scratch/stefan/7769890/working/building/REAL300000220054 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220054 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220054/0 /scratch/stefan/7769890/working/building/REAL300000220054 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/54 `/scratch/stefan/7769890/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(C)=C1OC(F)F) `REAL300000220054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220054 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(C)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 1, 12, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 35, 35, 35, 21, 33, 51, 88, 88, 35, 35, 35, 35, 11, 11, 2, 2, 2, 3, 3, 1, 35, 35, 35, 35, 88] 102 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 384 number of broken/clashed sets: 102 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220054 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(C)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 1, 12, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 35, 35, 35, 35, 35, 51, 69, 69, 35, 35, 35, 1, 1, 1, 1, 1, 2, 16, 16, 2, 2, 2, 1, 5, 5, 35, 35, 35, 51, 51, 35, 1, 2, 2, 2, 16] 102 rigid atoms, others: [0, 1, 2, 3, 4, 38, 18, 19, 20, 21, 22, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 275 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220054 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220054 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220054/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220054 Building REAL300000220055 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220055' /scratch/stefan/7769890/working/building/REAL300000220055 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220055 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220055/0 /scratch/stefan/7769890/working/building/REAL300000220055 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/55 `/scratch/stefan/7769890/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC2=C(C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1)OC(C)C2) `REAL300000220055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220055 none CCOC1=CC2=C(C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1)OC(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 140, 72, 72, 72, 72, 72, 72, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 72, 72, 72, 72, 169, 169, 169, 169, 169, 72, 72, 12, 12, 2, 2, 2, 3, 3, 1, 72, 72, 72, 72, 72, 72] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 391 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220055 none CCOC1=CC2=C(C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1)OC(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 72, 72, 72, 72, 72, 119, 162, 162, 72, 72, 72, 1, 1, 1, 1, 29, 29, 29, 29, 29, 1, 1, 9, 9, 72, 72, 72, 119, 119, 72, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 42, 46, 47, 23, 24, 25, 26] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 636 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220055 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220055 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220055/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220055 Building REAL300000220056 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220056' /scratch/stefan/7769890/working/building/REAL300000220056 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220056 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220056/0 /scratch/stefan/7769890/working/building/REAL300000220056 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/56 `/scratch/stefan/7769890/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=NC4=CC=CC=C4S3)O2)=N1) `REAL300000220056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220056 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=NC4=CC=CC=C4S3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 70, 70, 104, 130, 130, 71, 71, 71, 12, 12, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 1, 71, 71, 71, 71, 104, 104, 71, 13, 12, 1, 1, 13, 13, 12, 13] 201 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 418 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220056 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=NC4=CC=CC=C4S3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 71, 71, 71, 71, 167, 167, 167, 167, 167, 167, 167, 167, 70, 1, 2, 2, 2, 3, 3, 1, 12, 12, 71, 71, 167, 167, 167, 167] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 253 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220056 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=NC4=CC=CC=C4S3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 201, 201, 201, 167, 167, 167, 53, 53, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 167, 167, 167, 167, 201, 201, 167, 53, 53, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 466 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220056 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220056 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220056/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220056 Building REAL300000220057 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220057' /scratch/stefan/7769890/working/building/REAL300000220057 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220057 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220057/0 /scratch/stefan/7769890/working/building/REAL300000220057 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/57 `/scratch/stefan/7769890/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN1N=C(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Cl) `REAL300000220057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220057 none CCCCN1N=C(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'Cl', 'H', 'H', 'H', 'H', '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, 8, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 126, 41, 41, 41, 41, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 41, 41, 147, 147, 147, 147, 147, 147, 147, 126, 126, 41, 41, 41, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [44, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 559 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220057 none CCCCN1N=C(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'Cl', 'H', 'H', 'H', 'H', '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, 8, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 41, 41, 67, 96, 96, 41, 41, 41, 1, 1, 9, 9, 9, 9, 9, 9, 9, 5, 5, 2, 2, 2, 7, 7, 41, 41, 41, 67, 67, 41] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 24] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 372 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220057 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220057 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220057/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220057 Building REAL300000220058 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220058' /scratch/stefan/7769890/working/building/REAL300000220058 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220058 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220058/0 /scratch/stefan/7769890/working/building/REAL300000220058 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/58 `/scratch/stefan/7769890/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C) `REAL300000220058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220058 none CC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 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: [12, 11, 24, 24, 24, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 3, 3, 2, 2, 2, 1, 24, 24, 24, 24] 37 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 164 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: REAL300000220058 none CC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 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, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 24, 37, 37, 37, 24, 24, 24, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 9, 9, 37, 37, 24, 24, 24, 23, 1, 2, 2, 2] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 26, 38] set([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, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220058 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220058 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220058/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220058 Building REAL300000220059 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220059' /scratch/stefan/7769890/working/building/REAL300000220059 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220059 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220059/0 /scratch/stefan/7769890/working/building/REAL300000220059 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/59 `/scratch/stefan/7769890/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(=O)[O-]) `REAL300000220059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220059 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 26, 26, 26, 26, 116, 138, 157, 157, 47, 47, 47, 26, 8, 8, 2, 2, 2, 3, 3, 1, 26, 26, 138, 138] 201 rigid atoms, others: [38, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 424 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220059 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 26, 26, 26, 26, 26, 49, 83, 83, 26, 26, 26, 1, 1, 1, 1, 7, 20, 33, 33, 3, 3, 3, 1, 5, 5, 26, 26, 26, 49, 49, 26, 1, 1, 20, 20] 201 rigid atoms, others: [1, 2, 3, 4, 5, 39, 40, 19, 20, 21, 22, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 419 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220059 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220059 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220059/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220059 Building REAL300000220060 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220060' /scratch/stefan/7769890/working/building/REAL300000220060 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220060 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220060/0 /scratch/stefan/7769890/working/building/REAL300000220060 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/60 `/scratch/stefan/7769890/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=C(C)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220060 none CC1=NN(CC2=CC=C(C)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 10, 9, 9, 39, 39, 140, 140, 140, 140, 140, 201, 201, 201, 140, 140, 140, 10, 10, 10, 3, 3, 1, 1, 2, 2, 2, 1, 1, 10, 10, 10, 39, 39, 140, 140, 140, 201, 201, 140] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 40, 39] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 606 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220060 none CC1=NN(CC2=CC=C(C)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 10, 10, 8, 8, 10, 10, 1, 1, 1, 1, 7, 7, 45, 45, 45, 45, 45, 80, 90, 90, 45, 45, 45, 2, 2, 2, 5, 5, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 7, 7, 45, 45, 45, 80, 80, 45] 201 rigid atoms, others: [0, 1, 2, 3, 4, 12, 13, 14, 15] set([5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 363 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220060 none CC1=NN(CC2=CC=C(C)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 45, 45, 45, 128, 140, 140, 132, 132, 140, 140, 45, 45, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 45, 45, 45, 128, 128, 140, 140, 140, 140, 140, 140, 140, 45, 45, 45, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [51, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 564 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220060 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220060 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220060/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220060 Building REAL300000220061 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220061' /scratch/stefan/7769890/working/building/REAL300000220061 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220061 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220061/0 /scratch/stefan/7769890/working/building/REAL300000220061 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/61 `/scratch/stefan/7769890/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1O) `REAL300000220061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220061 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [59, 37, 37, 37, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 37, 37, 37, 37, 37, 59, 59, 59, 37, 11, 11, 2, 2, 2, 3, 3, 1, 37, 74] 152 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 197 number of broken/clashed sets: 152 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220061 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 1, 1, 1, 1, 5, 5, 37, 37, 37, 37, 37, 61, 76, 76, 37, 37, 37, 1, 1, 1, 1, 1, 4, 4, 4, 1, 5, 5, 37, 37, 37, 61, 61, 37, 1, 2] 152 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 36, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 262 number of broken/clashed sets: 152 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220061 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220061 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220061/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220061 Building REAL300000220062 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220062' /scratch/stefan/7769890/working/building/REAL300000220062 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220062 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220062/0 /scratch/stefan/7769890/working/building/REAL300000220062 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/62 `/scratch/stefan/7769890/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(Br)=C2)=N1) `REAL300000220062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220062 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 20, 20, 20, 32, 32, 32, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 32, 32, 20, 7, 7, 1, 1, 1] 32 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 106 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: REAL300000220062 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 7, 7, 1, 1, 1, 1, 1, 8, 8, 20, 20, 15, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 1, 8, 8, 20, 20, 20] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 88 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220062 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220062 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220062/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220062 Building REAL300000220063 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220063' /scratch/stefan/7769890/working/building/REAL300000220063 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220063 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220063/0 /scratch/stefan/7769890/working/building/REAL300000220063 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/63 `/scratch/stefan/7769890/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1O) `REAL300000220063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220063 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [172, 140, 53, 53, 53, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 53, 53, 53, 53, 53, 172, 172, 172, 172, 172, 53, 12, 12, 2, 2, 2, 3, 3, 1, 53, 106] 402 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 520 number of broken/clashed sets: 402 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220063 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 1, 1, 1, 1, 1, 7, 7, 53, 53, 53, 53, 53, 94, 132, 132, 53, 53, 53, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 1, 7, 7, 53, 53, 53, 94, 94, 53, 1, 2] 402 rigid atoms, others: [2, 3, 4, 5, 6, 39, 20, 21, 22, 23, 24, 30] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 540 number of broken/clashed sets: 402 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220063 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220063 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220063/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220063 Building REAL300000220064 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220064' /scratch/stefan/7769890/working/building/REAL300000220064 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220064 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220064/0 /scratch/stefan/7769890/working/building/REAL300000220064 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/64 `/scratch/stefan/7769890/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC#N)N1) `REAL300000220064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220064 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC#N)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 99, 151, 151, 58, 58, 58, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 8, 34, 34, 58, 58, 58, 58, 99, 99, 9, 9, 1, 1, 1, 1, 34, 34, 58] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 620 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220064 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC#N)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 58, 58, 23, 58, 58, 58, 106, 169, 169, 1, 2, 2, 2, 3, 3, 11, 11, 58, 58, 58, 58, 169, 169, 1] 201 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 588 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220064 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220064 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220064/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220064 Building REAL300000220065 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220065' /scratch/stefan/7769890/working/building/REAL300000220065 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220065 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220065/0 /scratch/stefan/7769890/working/building/REAL300000220065 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/65 `/scratch/stefan/7769890/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1OC) `REAL300000220065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220065 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [77, 39, 39, 39, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 39, 39, 39, 39, 39, 83, 77, 77, 77, 39, 12, 12, 2, 2, 2, 3, 3, 1, 39, 83, 83, 83] 118 rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 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: 221 number of broken/clashed sets: 118 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220065 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 39, 39, 39, 39, 39, 65, 82, 82, 39, 39, 39, 1, 1, 1, 1, 1, 6, 4, 4, 4, 1, 5, 5, 39, 39, 39, 65, 65, 39, 1, 7, 7, 7] 118 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 28, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 294 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220065 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220065 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220065/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220065 Building REAL300000220066 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220066' /scratch/stefan/7769890/working/building/REAL300000220066 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220066 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220066/0 /scratch/stefan/7769890/working/building/REAL300000220066 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/66 `/scratch/stefan/7769890/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(O)C(Br)=C2)=N1) `REAL300000220066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220066 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(O)C(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 32, 32, 32, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 32, 32, 20, 7, 7, 1, 1, 2, 1] 64 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 108 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220066 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(O)C(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 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 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, 1, 3, 6, 6, 1, 1, 1, 1, 1, 8, 8, 20, 20, 15, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 1, 8, 8, 20, 20, 40, 20] 64 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 126 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220066 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220066 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220066/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220066 Building REAL300000220067 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220067' /scratch/stefan/7769890/working/building/REAL300000220067 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220067 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220067/0 /scratch/stefan/7769890/working/building/REAL300000220067 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/67 `/scratch/stefan/7769890/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC(C)C) `REAL300000220067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220067 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 75, 98, 129, 129, 39, 39, 39, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 98, 98, 129, 129, 129, 129, 129, 129, 129] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 489 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220067 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 39, 70, 70, 21, 21, 21, 1, 1, 1, 6, 8, 14, 14, 3, 3, 3, 1, 1, 5, 5, 21, 21, 21, 39, 39, 21, 1, 8, 8, 14, 14, 14, 14, 14, 14, 14] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 20, 21, 22, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 320 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220067 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220067 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220067/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220067 Building REAL300000220068 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220068' /scratch/stefan/7769890/working/building/REAL300000220068 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220068 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220068/0 /scratch/stefan/7769890/working/building/REAL300000220068 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/68 `/scratch/stefan/7769890/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC) `REAL300000220068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220068 none CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 117, 40, 40, 40, 40, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 40, 40, 56, 153, 153, 153, 153, 153, 40, 40, 40, 9, 9, 3, 3, 2, 2, 2, 1, 56, 56, 56] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 422 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: REAL300000220068 none CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 40, 40, 40, 40, 40, 65, 102, 102, 40, 40, 40, 1, 1, 5, 25, 25, 25, 24, 24, 1, 1, 1, 9, 9, 65, 65, 40, 40, 40, 40, 5, 5, 5] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 22, 23, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 439 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220068 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220068 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220068/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220068 Building REAL300000220069 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220069' /scratch/stefan/7769890/working/building/REAL300000220069 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220069 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220069/0 /scratch/stefan/7769890/working/building/REAL300000220069 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/69 `/scratch/stefan/7769890/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC) `REAL300000220069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220069 none CCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 105, 92, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 21, 39, 140, 140, 140, 140, 140, 105, 105, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 21, 39, 39, 39] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 469 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220069 none CCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 11, 9, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 40, 75, 75, 21, 21, 21, 1, 1, 1, 1, 3, 20, 20, 20, 20, 20, 11, 11, 1, 5, 5, 21, 21, 21, 40, 40, 21, 1, 1, 3, 3, 3] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 42, 43, 21, 22, 23, 24] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 354 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220069 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220069 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220069/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220069 Building REAL300000220070 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220070' /scratch/stefan/7769890/working/building/REAL300000220070 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220070 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220070/0 /scratch/stefan/7769890/working/building/REAL300000220070 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/70 `/scratch/stefan/7769890/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)S2)=N1) `REAL300000220070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220070 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [27, 27, 27, 27, 32, 32, 32, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 32, 32, 27, 9, 9, 1, 1] 32 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 74 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: REAL300000220070 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 1, 9, 9, 27, 27] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 69 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220070 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220070 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220070/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220070 Building REAL300000220071 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220071' /scratch/stefan/7769890/working/building/REAL300000220071 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220071 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220071/0 /scratch/stefan/7769890/working/building/REAL300000220071 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/71 `/scratch/stefan/7769890/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N=C3C=CC=CN32)N1) `REAL300000220071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220071 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N=C3C=CC=CN32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [35, 35, 35, 35, 51, 51, 51, 31, 35, 35, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 51, 51, 9, 9, 1, 1, 1, 1, 35] 51 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 161 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: REAL300000220071 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N=C3C=CC=CN32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 10, 10, 35, 35, 29, 35, 1] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220071 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220071 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220071/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220071 Building REAL300000220072 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220072' /scratch/stefan/7769890/working/building/REAL300000220072 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220072 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220072/0 /scratch/stefan/7769890/working/building/REAL300000220072 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/72 `/scratch/stefan/7769890/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1OC) `REAL300000220072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220072 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 130, 32, 32, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 32, 32, 32, 32, 32, 68, 160, 160, 160, 160, 160, 32, 9, 9, 2, 2, 2, 3, 3, 1, 32, 68, 68, 68] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 448 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220072 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 9, 1, 1, 1, 1, 1, 5, 5, 32, 32, 32, 32, 32, 58, 92, 92, 32, 32, 32, 1, 1, 1, 1, 1, 4, 27, 27, 27, 27, 27, 1, 5, 5, 32, 32, 32, 58, 58, 32, 1, 4, 4, 4] 201 rigid atoms, others: [2, 3, 4, 5, 6, 40, 20, 21, 22, 23, 24, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 417 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220072 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220072 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220072/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220072 Building REAL300000220073 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220073' /scratch/stefan/7769890/working/building/REAL300000220073 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220073 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220073/0 /scratch/stefan/7769890/working/building/REAL300000220073 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/73 `/scratch/stefan/7769890/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC) `REAL300000220073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220073 none C#CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 61, 26, 26, 26, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 26, 26, 26, 47, 85, 146, 146, 146, 26, 26, 9, 9, 2, 2, 2, 3, 3, 1, 26, 85, 85, 85, 85, 85] 201 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 679 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220073 none C#CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 5, 1, 1, 1, 1, 1, 1, 5, 5, 26, 26, 26, 26, 26, 43, 66, 66, 26, 26, 26, 1, 1, 1, 3, 11, 19, 19, 19, 1, 1, 5, 5, 26, 26, 26, 43, 43, 26, 1, 11, 11, 12, 12, 12] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 40, 22, 23, 24, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 314 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220073 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220073 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220073/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220073 Building REAL300000220074 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220074' /scratch/stefan/7769890/working/building/REAL300000220074 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220074 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220074/0 /scratch/stefan/7769890/working/building/REAL300000220074 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/74 `/scratch/stefan/7769890/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220074 none C=CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 106, 96, 30, 30, 30, 30, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 30, 154, 154, 154, 106, 106, 30, 30, 30, 10, 10, 3, 3, 2, 2, 2, 1, 30] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 406 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220074 none C=CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 12, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 30, 30, 30, 30, 30, 56, 91, 91, 30, 30, 30, 1, 36, 36, 36, 12, 12, 1, 1, 1, 5, 5, 56, 56, 30, 30, 30, 30, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 40, 23, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 432 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220074 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220074 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220074/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220074 Building REAL300000220075 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220075' /scratch/stefan/7769890/working/building/REAL300000220075 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220075 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220075/0 /scratch/stefan/7769890/working/building/REAL300000220075 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/75 `/scratch/stefan/7769890/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC(C)C) `REAL300000220075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220075 none COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 51, 51, 51, 51, 51, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 51, 51, 120, 161, 161, 93, 93, 93, 51, 51, 51, 10, 10, 3, 3, 2, 2, 2, 1, 161, 161, 161, 161, 161, 161, 161] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 501 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: REAL300000220075 none COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 51, 51, 51, 51, 51, 86, 142, 142, 51, 51, 51, 1, 1, 4, 10, 10, 4, 4, 4, 1, 1, 1, 9, 9, 86, 86, 51, 51, 51, 51, 10, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 558 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220075 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220075 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220075/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220075 Building REAL300000220076 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220076' /scratch/stefan/7769890/working/building/REAL300000220076 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220076 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220076/0 /scratch/stefan/7769890/working/building/REAL300000220076 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/76 `/scratch/stefan/7769890/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=C(Cl)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220076 none CCOC1=C(Cl)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 85, 48, 48, 48, 48, 48, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 48, 48, 48, 110, 163, 163, 163, 163, 163, 48, 12, 12, 2, 2, 2, 3, 3, 1, 48, 110, 110, 110] 201 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 679 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220076 none CCOC1=C(Cl)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 48, 48, 48, 48, 48, 85, 117, 117, 48, 48, 48, 1, 1, 1, 3, 12, 12, 12, 12, 12, 1, 5, 5, 48, 48, 48, 85, 85, 48, 1, 4, 4, 4] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 40, 22, 23, 24, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 455 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220076 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220076 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220076/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220076 Building REAL300000220077 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220077' /scratch/stefan/7769890/working/building/REAL300000220077 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220077 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220077/0 /scratch/stefan/7769890/working/building/REAL300000220077 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/77 `/scratch/stefan/7769890/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=CC=C1OCC) `REAL300000220077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220077 none CCCOC1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=CC=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 56, 40, 32, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 32, 32, 32, 32, 32, 87, 114, 99, 99, 99, 99, 99, 56, 56, 9, 9, 2, 2, 2, 3, 3, 1, 32, 32, 32, 114, 114, 114, 114, 114] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 613 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220077 none CCCOC1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=CC=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 3, 1, 1, 1, 1, 9, 9, 32, 32, 32, 32, 32, 42, 72, 72, 32, 32, 32, 1, 1, 1, 1, 1, 7, 23, 13, 13, 13, 13, 13, 7, 7, 9, 9, 32, 32, 32, 42, 42, 32, 1, 1, 1, 23, 23, 23, 23, 23] 201 rigid atoms, others: [3, 4, 5, 6, 42, 43, 44, 20, 21, 22, 23, 24] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 49]) total number of confs: 348 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220077 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220077 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220077/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220077 Building REAL300000220078 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220078' /scratch/stefan/7769890/working/building/REAL300000220078 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220078 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220078/0 /scratch/stefan/7769890/working/building/REAL300000220078 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/78 `/scratch/stefan/7769890/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC) `REAL300000220078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220078 none CCCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 90, 83, 20, 20, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 20, 20, 20, 20, 37, 147, 147, 147, 147, 147, 147, 147, 90, 90, 20, 5, 5, 2, 2, 2, 3, 3, 1, 20, 20, 37, 37, 37] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 505 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220078 none CCCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 9, 7, 1, 1, 1, 1, 1, 5, 5, 20, 20, 20, 20, 20, 36, 57, 57, 20, 20, 20, 1, 1, 1, 1, 3, 20, 20, 20, 20, 20, 20, 20, 9, 9, 1, 5, 5, 20, 20, 20, 36, 36, 20, 1, 1, 3, 3, 3] 201 rigid atoms, others: [36, 5, 6, 7, 8, 45, 46, 25, 22, 23, 24, 4] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 286 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220078 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220078 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220078/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220078 Building REAL300000220079 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220079' /scratch/stefan/7769890/working/building/REAL300000220079 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220079 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220079/0 /scratch/stefan/7769890/working/building/REAL300000220079 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/79 `/scratch/stefan/7769890/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220079 none CCCCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 130, 130, 52, 52, 11, 11, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 52, 52, 21, 21, 6, 6, 2, 2, 2, 3, 3, 1, 21, 21] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 55, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 56, 57]) total number of confs: 500 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220079 none CCCCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 37, 47, 47, 21, 21, 21, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 1, 5, 5, 21, 21, 21, 37, 37, 21, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 46, 47, 56, 57, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 198 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220079 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220079 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220079/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220079 Building REAL300000220080 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220080' /scratch/stefan/7769890/working/building/REAL300000220080 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220080 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220080/0 /scratch/stefan/7769890/working/building/REAL300000220080 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/80 `/scratch/stefan/7769890/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220080 none CC(=O)NC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 41, 41, 17, 10, 24, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 24, 24, 41, 41, 41, 41, 24, 24, 10, 10, 3, 3, 2, 2, 2, 1, 24, 24] 53 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 179 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: REAL300000220080 none CC(=O)NC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 34, 40, 40, 24, 24, 24, 1, 1, 3, 3, 3, 3, 1, 1, 6, 6, 34, 34, 24, 24, 24, 24, 1, 1] 53 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 22, 23, 38, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220080 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220080 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220080/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220080 Building REAL300000220081 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220081' /scratch/stefan/7769890/working/building/REAL300000220081 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220081 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220081/0 /scratch/stefan/7769890/working/building/REAL300000220081 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/81 `/scratch/stefan/7769890/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2Cl)N1) `REAL300000220081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220081 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [29, 29, 29, 29, 35, 35, 35, 29, 29, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 35, 35, 9, 9, 1, 1, 1, 1, 29] 35 rigid atoms, others: [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, 32, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 81 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220081 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 29, 29, 21, 29, 29, 29, 1, 2, 2, 2, 3, 3, 11, 11, 29, 29, 25, 29, 1] 35 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 20] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 102 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220081 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220081 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220081/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220081 Building REAL300000220082 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220082' /scratch/stefan/7769890/working/building/REAL300000220082 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220082 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220082/0 /scratch/stefan/7769890/working/building/REAL300000220082 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/82 `/scratch/stefan/7769890/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC([N+](=O)[O-])=C2)N1) `REAL300000220082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220082 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC([N+](=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 33, 33, 33, 25, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 25, 25, 25, 33, 33, 6, 6, 1, 1, 1, 1, 25] 33 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 89 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220082 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC([N+](=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 25, 25, 23, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 9, 9, 25, 25, 23, 25, 1] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220082 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220082 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220082/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220082 Building REAL300000220083 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220083' /scratch/stefan/7769890/working/building/REAL300000220083 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220083 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220083/0 /scratch/stefan/7769890/working/building/REAL300000220083 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/83 `/scratch/stefan/7769890/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([N+](=O)[O-])C=C2)N1) `REAL300000220083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220083 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([N+](=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 13] 13 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 19 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: REAL300000220083 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([N+](=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 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: [1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 10, 10, 13, 13, 10, 10, 13, 13, 13, 13, 1, 2, 2, 2, 3, 3, 10, 10, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 63 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220083 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220083 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220083/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220083 Building REAL300000220084 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220084' /scratch/stefan/7769890/working/building/REAL300000220084 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220084 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220084/0 /scratch/stefan/7769890/working/building/REAL300000220084 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/84 `/scratch/stefan/7769890/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=CC=CC=C23)N1) `REAL300000220084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220084 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [29, 29, 29, 29, 41, 41, 41, 29, 29, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 41, 41, 7, 7, 1, 1, 1, 1, 1, 1, 1, 29] 41 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 113 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: REAL300000220084 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 2, 2, 2, 3, 3, 9, 9, 29, 29, 29, 29, 29, 29, 29, 1] 41 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 71 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220084 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220084 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220084/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220084 Building REAL300000220085 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220085' /scratch/stefan/7769890/working/building/REAL300000220085 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220085 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220085/0 /scratch/stefan/7769890/working/building/REAL300000220085 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/85 `/scratch/stefan/7769890/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N(C)C)C=C2)N1) `REAL300000220085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220085 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 15, 15, 21, 21, 21, 15, 15, 15, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 15, 15, 15, 15, 21, 21, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 15] 25 rigid atoms, others: [38, 39, 12, 13, 14, 15, 16, 17, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 67 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: REAL300000220085 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 15, 15, 9, 13, 25, 25, 15, 15, 1, 2, 2, 2, 3, 3, 9, 9, 15, 15, 25, 25, 25, 25, 25, 25, 15, 15, 1] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 40, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220085 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220085 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220085/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220085 Building REAL300000220086 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220086' /scratch/stefan/7769890/working/building/REAL300000220086 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220086 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220086/0 /scratch/stefan/7769890/working/building/REAL300000220086 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/86 `/scratch/stefan/7769890/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220086 none CCN(CC)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [93, 52, 12, 52, 96, 12, 22, 22, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 22, 22, 93, 93, 93, 93, 93, 96, 96, 96, 96, 96, 22, 22, 12, 12, 3, 3, 2, 2, 2, 1, 22, 22] 185 rigid atoms, others: [44, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 609 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: REAL300000220086 none CCN(CC)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 6, 1, 6, 24, 1, 1, 1, 1, 1, 5, 5, 24, 24, 24, 24, 24, 38, 58, 58, 24, 24, 24, 1, 1, 20, 20, 20, 20, 20, 24, 24, 24, 24, 24, 1, 1, 5, 5, 38, 38, 24, 24, 24, 24, 1, 1] 174 rigid atoms, others: [2, 35, 36, 5, 6, 7, 8, 9, 45, 46, 23, 24] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 336 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220086 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220086 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220086/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220086 Building REAL300000220087 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220087' /scratch/stefan/7769890/working/building/REAL300000220087 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220087 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220087/0 /scratch/stefan/7769890/working/building/REAL300000220087 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/87 `/scratch/stefan/7769890/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2)=N1) `REAL300000220087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220087 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [8, 8, 8, 8, 14, 14, 14, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 8, 4, 4, 1, 1, 1, 1] 14 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 52 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: REAL300000220087 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 3, 3, 1, 8, 8, 8, 8, 8, 8] 14 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 40 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220087 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220087 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220087/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220087 Building REAL300000220088 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220088' /scratch/stefan/7769890/working/building/REAL300000220088 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220088 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220088/0 /scratch/stefan/7769890/working/building/REAL300000220088 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/88 `/scratch/stefan/7769890/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)C=C2)N1) `REAL300000220088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220088 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 13] 13 rigid atoms, others: [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, 32, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 19 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: REAL300000220088 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 9, 9, 13, 13, 9, 11, 13, 13, 1, 2, 2, 2, 3, 3, 9, 9, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 20] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 55 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220088 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220088 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220088/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220088 Building REAL300000220089 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220089' /scratch/stefan/7769890/working/building/REAL300000220089 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220089 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220089/0 /scratch/stefan/7769890/working/building/REAL300000220089 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/89 `/scratch/stefan/7769890/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(OC)=C1OC) `REAL300000220089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220089 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(OC)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [63, 28, 28, 28, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 28, 28, 28, 66, 12, 12, 93, 63, 63, 63, 28, 12, 12, 2, 2, 2, 3, 3, 1, 28, 66, 66, 66, 93, 93, 93] 139 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 322 number of broken/clashed sets: 139 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220089 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(OC)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 4, 4, 28, 28, 28, 28, 28, 48, 76, 76, 28, 28, 28, 1, 1, 1, 3, 1, 1, 6, 4, 4, 4, 1, 4, 4, 28, 28, 28, 48, 48, 28, 1, 3, 3, 3, 7, 7, 7] 139 rigid atoms, others: [1, 2, 3, 4, 5, 38, 19, 20, 21, 23, 24, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 291 number of broken/clashed sets: 139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220089 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220089 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220089/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220089 Building REAL300000220090 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220090' /scratch/stefan/7769890/working/building/REAL300000220090 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220090 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220090/0 /scratch/stefan/7769890/working/building/REAL300000220090 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/90 `/scratch/stefan/7769890/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(F)C=CC=C2Cl)N1) `REAL300000220090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220090 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(F)C=CC=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [31, 31, 31, 31, 41, 41, 41, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 41, 41, 9, 9, 1, 1, 1, 31] 41 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 107 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220090 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(F)C=CC=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 31, 31, 31, 21, 31, 31, 31, 1, 2, 2, 2, 3, 3, 10, 10, 31, 21, 31, 1] 41 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 101 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220090 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220090 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220090/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220090 Building REAL300000220091 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220091' /scratch/stefan/7769890/working/building/REAL300000220091 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220091 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220091/0 /scratch/stefan/7769890/working/building/REAL300000220091 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/91 `/scratch/stefan/7769890/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCCOC3=C2)N1) `REAL300000220091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220091 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCCOC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 4, 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: [18, 18, 18, 18, 27, 27, 27, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 27, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 18] 27 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 83 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: REAL300000220091 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCCOC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 3, 8, 8, 18, 18, 18, 18, 18, 18, 18, 1] 27 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220091 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220091 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220091/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220091 Building REAL300000220092 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220092' /scratch/stefan/7769890/working/building/REAL300000220092 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220092 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220092/0 /scratch/stefan/7769890/working/building/REAL300000220092 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/92 `/scratch/stefan/7769890/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC(F)F)N1) `REAL300000220092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220092 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC(F)F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 97, 132, 132, 58, 58, 58, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 42, 42, 58, 58, 58, 58, 97, 97, 9, 9, 1, 1, 1, 1, 42, 58] 193 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 580 number of broken/clashed sets: 193 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220092 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC(F)F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 58, 58, 20, 58, 58, 58, 125, 172, 172, 1, 2, 2, 2, 3, 3, 12, 12, 58, 58, 58, 58, 172, 1] 193 rigid atoms, others: [0, 1, 2, 3, 36, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 587 number of broken/clashed sets: 193 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220092 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220092 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220092/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220092 Building REAL300000220093 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220093' /scratch/stefan/7769890/working/building/REAL300000220093 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220093 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220093/0 /scratch/stefan/7769890/working/building/REAL300000220093 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/93 `/scratch/stefan/7769890/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Br)=C2)=N1) `REAL300000220093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220093 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [18, 18, 18, 18, 32, 32, 32, 18, 18, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 32, 32, 18, 7, 7, 1, 1, 1, 1] 32 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 116 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: REAL300000220093 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 7, 7, 1, 1, 1, 1, 1, 7, 7, 18, 18, 13, 18, 18, 18, 1, 2, 2, 2, 3, 3, 1, 7, 7, 18, 18, 18, 18] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 84 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220093 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220093 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220093/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220093 Building REAL300000220094 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220094' /scratch/stefan/7769890/working/building/REAL300000220094 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220094 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220094/0 /scratch/stefan/7769890/working/building/REAL300000220094 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/94 `/scratch/stefan/7769890/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2[N+](=O)[O-])N1) `REAL300000220094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220094 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2[N+](=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 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, 26, 26, 26, 35, 35, 35, 26, 26, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 26, 26, 26, 26, 35, 35, 7, 7, 1, 1, 1, 1, 26] 35 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 96 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: REAL300000220094 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2[N+](=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 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, 3, 6, 6, 1, 1, 1, 1, 1, 10, 10, 26, 26, 18, 26, 26, 26, 26, 26, 1, 2, 2, 2, 3, 3, 10, 10, 26, 26, 18, 26, 1] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 90 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220094 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220094 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220094/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220094 Building REAL300000220095 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220095' /scratch/stefan/7769890/working/building/REAL300000220095 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220095 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220095/0 /scratch/stefan/7769890/working/building/REAL300000220095 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/95 `/scratch/stefan/7769890/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC) `REAL300000220095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220095 none COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [131, 70, 70, 70, 70, 70, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 70, 70, 136, 131, 131, 131, 70, 70, 70, 12, 12, 3, 3, 2, 2, 2, 1, 136, 136, 136] 179 rigid atoms, others: [37, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 331 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: REAL300000220095 none COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 70, 70, 70, 70, 70, 107, 156, 156, 70, 70, 70, 1, 1, 7, 4, 4, 4, 1, 1, 1, 9, 9, 107, 107, 70, 70, 70, 70, 7, 7, 7] 179 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 512 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220095 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220095 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220095/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220095 Building REAL300000220096 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220096' /scratch/stefan/7769890/working/building/REAL300000220096 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220096 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220096/0 /scratch/stefan/7769890/working/building/REAL300000220096 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/96 `/scratch/stefan/7769890/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C=C2Cl)=N1) `REAL300000220096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220096 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [15, 15, 15, 15, 27, 27, 27, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 27, 27, 15, 7, 7, 1, 1, 1] 27 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 99 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: REAL300000220096 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 3, 1, 9, 9, 15, 15, 15] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 54 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220096 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220096 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220096/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220096 Building REAL300000220097 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220097' /scratch/stefan/7769890/working/building/REAL300000220097 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220097 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220097/0 /scratch/stefan/7769890/working/building/REAL300000220097 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/97 `/scratch/stefan/7769890/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C=C2)=N1) `REAL300000220097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220097 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 31, 50, 50, 19, 19, 19, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 19, 19, 19, 19, 31, 31, 19, 4, 4, 1, 1, 10, 10, 10, 11, 10, 11, 10, 10, 1, 1] 63 rigid atoms, others: [34, 35, 44, 45, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 189 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: REAL300000220097 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 19, 19, 11, 11, 52, 52, 52, 52, 52, 19, 19, 1, 2, 2, 2, 3, 3, 1, 11, 11, 19, 19, 52, 52, 52, 52, 52, 52, 52, 52, 19, 19] 63 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 131 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220097 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 63, 63, 63, 52, 52, 52, 19, 19, 2, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 52, 52, 52, 52, 63, 63, 52, 19, 19, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 63 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45]) total number of confs: 173 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220097 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220097 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220097/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220097 Building REAL300000220098 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220098' /scratch/stefan/7769890/working/building/REAL300000220098 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220098 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220098/0 /scratch/stefan/7769890/working/building/REAL300000220098 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/98 `/scratch/stefan/7769890/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1OC) `REAL300000220098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220098 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [70, 35, 35, 35, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 35, 35, 35, 67, 70, 70, 70, 35, 35, 11, 11, 3, 3, 2, 2, 2, 1, 35, 67, 67, 67] 109 rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 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: 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: REAL300000220098 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 56, 85, 85, 35, 35, 35, 1, 1, 1, 3, 4, 4, 4, 1, 1, 7, 7, 56, 56, 35, 35, 35, 35, 1, 4, 4, 4] 109 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 27, 28, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 309 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220098 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220098 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220098/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220098 Building REAL300000220099 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220099' /scratch/stefan/7769890/working/building/REAL300000220099 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220099 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220099/0 /scratch/stefan/7769890/working/building/REAL300000220099 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/99 `/scratch/stefan/7769890/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220099 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 17, 21, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 10, 10, 3, 3, 2, 2, 2, 1, 21, 21] 25 rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 76 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: REAL300000220099 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 25, 25, 25, 21, 21, 21, 1, 1, 2, 2, 2, 1, 1, 6, 6, 25, 25, 21, 21, 21, 21, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 20, 21, 25, 26, 36] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 63 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220099 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220099 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220099/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220099 Building REAL300000220100 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220100' /scratch/stefan/7769890/working/building/REAL300000220100 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220100 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220100/0 /scratch/stefan/7769890/working/building/REAL300000220100 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/100 `/scratch/stefan/7769890/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1) `REAL300000220100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220100 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [108, 68, 35, 68, 68, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 68, 68, 89, 68, 108, 108, 108, 68, 68, 11, 11, 3, 3, 2, 2, 2, 1, 89, 89, 89, 68] 157 rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40]) total number of confs: 358 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: REAL300000220100 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 12, 12, 68, 68, 68, 68, 68, 103, 137, 137, 68, 68, 68, 1, 1, 3, 1, 3, 3, 3, 1, 1, 12, 12, 103, 103, 68, 68, 68, 68, 3, 3, 3, 1] 157 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 20, 21, 23, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 448 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220100 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220100 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220100/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220100 Building REAL300000220101 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220101' /scratch/stefan/7769890/working/building/REAL300000220101 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220101 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220101/0 /scratch/stefan/7769890/working/building/REAL300000220101 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/101 `/scratch/stefan/7769890/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(OC(F)F)C=CC3=CC=CC=C32)N1) `REAL300000220101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220101 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(OC(F)F)C=CC3=CC=CC=C32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 73, 117, 117, 41, 41, 41, 7, 7, 1, 1, 1, 1, 7, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 73, 73, 7, 7, 41, 1, 1, 1, 1, 1, 1, 41] 145 rigid atoms, others: [36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42]) total number of confs: 538 number of broken/clashed sets: 144 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220101 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(OC(F)F)C=CC3=CC=CC=C32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 41, 41, 82, 127, 127, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 3, 3, 11, 11, 127, 41, 41, 41, 41, 41, 41, 1] 145 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 27, 42] set([4, 5, 6, 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, 41]) total number of confs: 393 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220101 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220101 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220101/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220101 Building REAL300000220102 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220102' /scratch/stefan/7769890/working/building/REAL300000220102 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220102 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220102/0 /scratch/stefan/7769890/working/building/REAL300000220102 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/102 `/scratch/stefan/7769890/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1OC) `REAL300000220102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220102 none CCOC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 116, 32, 32, 32, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 32, 32, 32, 32, 67, 138, 138, 138, 138, 138, 32, 10, 10, 3, 3, 2, 2, 2, 1, 32, 32, 67, 67, 67] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 375 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: REAL300000220102 none CCOC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 1, 1, 1, 1, 1, 5, 5, 32, 32, 32, 32, 32, 59, 92, 92, 32, 32, 32, 1, 1, 1, 1, 3, 23, 23, 23, 23, 23, 1, 5, 5, 59, 59, 32, 32, 32, 32, 1, 1, 4, 4, 4] 201 rigid atoms, others: [2, 3, 4, 5, 6, 39, 40, 20, 21, 22, 23, 30] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 414 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220102 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220102 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220102/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220102 Building REAL300000220103 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220103' /scratch/stefan/7769890/working/building/REAL300000220103 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220103 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220103/0 /scratch/stefan/7769890/working/building/REAL300000220103 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/103 `/scratch/stefan/7769890/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC2=CC=CC=C2)N1) `REAL300000220103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220103 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 62, 78, 78, 37, 37, 37, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 41, 41, 31, 41, 41, 37, 37, 37, 37, 62, 62, 9, 9, 1, 1, 1, 1, 22, 22, 41, 41, 41, 41, 41, 37] 201 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 406 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220103 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 6, 6, 37, 37, 13, 37, 37, 37, 74, 141, 154, 154, 152, 154, 154, 1, 2, 2, 2, 3, 3, 6, 6, 37, 37, 37, 37, 141, 141, 154, 154, 154, 154, 154, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 46, 27] set([4, 5, 6, 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, 41, 42, 43, 44, 45]) total number of confs: 573 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220103 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 154, 154, 154, 201, 201, 201, 154, 154, 154, 112, 112, 41, 41, 41, 41, 41, 41, 15, 3, 1, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 201, 201, 112, 112, 41, 41, 41, 41, 3, 3, 1, 1, 1, 1, 1, 154] 201 rigid atoms, others: [41, 42, 43, 44, 45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 620 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220103 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220103 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220103/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220103 Building REAL300000220104 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220104' /scratch/stefan/7769890/working/building/REAL300000220104 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220104 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220104/0 /scratch/stefan/7769890/working/building/REAL300000220104 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/104 `/scratch/stefan/7769890/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220104 none CCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 64, 57, 16, 16, 25, 25, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 25, 25, 127, 127, 127, 127, 127, 127, 127, 127, 127, 64, 64, 25, 25, 10, 10, 2, 2, 2, 3, 3, 1, 25, 25] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 495 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220104 none CCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 5, 5, 25, 25, 25, 25, 25, 45, 67, 67, 25, 25, 25, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 1, 1, 5, 5, 25, 25, 25, 45, 45, 25, 1, 1] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 47, 48, 24, 25, 38, 5] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 301 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220104 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220104 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220104/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220104 Building REAL300000220105 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220105' /scratch/stefan/7769890/working/building/REAL300000220105 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220105 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220105/0 /scratch/stefan/7769890/working/building/REAL300000220105 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/105 `/scratch/stefan/7769890/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C2NC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C2=CC=C1) `REAL300000220105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220105 none CCC1=C2NC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [88, 58, 58, 58, 58, 58, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 58, 58, 58, 58, 88, 88, 88, 88, 88, 58, 58, 12, 12, 3, 3, 2, 2, 2, 1, 58, 58, 58] 121 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 286 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: REAL300000220105 none CCC1=C2NC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 58, 58, 58, 58, 58, 88, 94, 94, 58, 58, 58, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 11, 12, 88, 88, 58, 58, 58, 58, 1, 1, 1] 121 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 40, 41, 42, 21, 22, 23, 24, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 305 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220105 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220105 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220105/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220105 Building REAL300000220106 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220106' /scratch/stefan/7769890/working/building/REAL300000220106 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220106 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220106/0 /scratch/stefan/7769890/working/building/REAL300000220106 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/106 `/scratch/stefan/7769890/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)O2)=N1) `REAL300000220106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220106 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [42, 41, 42, 42, 62, 94, 94, 42, 42, 42, 9, 9, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 12, 12, 12, 1, 41, 42, 42, 42, 62, 62, 42, 9, 9, 1, 1, 12, 12, 1, 12] 201 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 334 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220106 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 42, 42, 42, 42, 151, 151, 42, 151, 151, 151, 151, 151, 42, 1, 2, 2, 2, 3, 3, 1, 11, 11, 42, 42, 151, 151, 52, 151] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 407 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220106 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [151, 151, 151, 151, 201, 201, 201, 151, 151, 151, 41, 41, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 151, 151, 151, 151, 201, 201, 151, 41, 41, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 526 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220106 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220106 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220106/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220106 Building REAL300000220107 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220107' /scratch/stefan/7769890/working/building/REAL300000220107 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220107 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220107/0 /scratch/stefan/7769890/working/building/REAL300000220107 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/107 `/scratch/stefan/7769890/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)O2)=N1) `REAL300000220107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220107 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 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: [66, 65, 66, 66, 92, 98, 98, 66, 66, 66, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 1, 2, 7, 7, 7, 7, 1, 65, 66, 66, 66, 92, 92, 66, 13, 13, 1, 1, 7, 7, 7, 7] 143 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 302 number of broken/clashed sets: 142 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220107 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 66, 66, 66, 66, 120, 120, 66, 73, 120, 120, 120, 120, 66, 1, 2, 2, 2, 3, 3, 1, 12, 12, 66, 66, 120, 120, 120, 120] 143 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 495 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220107 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 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: [120, 120, 120, 120, 143, 143, 143, 120, 120, 120, 51, 51, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 120, 120, 120, 120, 143, 143, 120, 51, 51, 7, 7, 1, 1, 1, 1] 143 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 346 number of broken/clashed sets: 142 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220107 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220107 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220107/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220107 Building REAL300000220108 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220108' /scratch/stefan/7769890/working/building/REAL300000220108 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220108 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220108/0 /scratch/stefan/7769890/working/building/REAL300000220108 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/108 `/scratch/stefan/7769890/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1) `REAL300000220108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220108 none COC(=O)C1=CC=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 9, 35, 9, 9, 7, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 29, 41, 41, 17, 17, 17, 1, 35, 35, 35, 9, 9, 9, 9, 1, 1, 3, 3, 18, 18, 18, 29, 29, 17] 201 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 231 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220108 none COC(=O)C1=CC=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 18, 18, 78, 78, 78, 78, 78, 131, 152, 152, 78, 78, 78, 9, 9, 9, 9, 1, 1, 1, 1, 9, 9, 18, 18, 78, 78, 78, 131, 131, 78] 201 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 34] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 532 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220108 none COC(=O)C1=CC=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 78, 142, 78, 78, 76, 78, 78, 17, 17, 17, 17, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 17, 142, 142, 142, 78, 78, 78, 78, 17, 17, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 360 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220108 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220108 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220108/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220108 Building REAL300000220109 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220109' /scratch/stefan/7769890/working/building/REAL300000220109 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220109 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220109/0 /scratch/stefan/7769890/working/building/REAL300000220109 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/109 `/scratch/stefan/7769890/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Br) `REAL300000220109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220109 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [43, 27, 19, 27, 27, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 27, 27, 27, 43, 43, 43, 27, 27, 11, 11, 2, 2, 2, 3, 3, 1, 27] 63 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 142 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: REAL300000220109 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [3, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 44, 63, 63, 27, 27, 27, 1, 1, 1, 4, 4, 4, 1, 1, 6, 6, 27, 27, 27, 44, 44, 27, 1] 63 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 226 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220109 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220109 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220109/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220109 Building REAL300000220110 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220110' /scratch/stefan/7769890/working/building/REAL300000220110 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220110 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220110/0 /scratch/stefan/7769890/working/building/REAL300000220110 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/110 `/scratch/stefan/7769890/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC(C)C)N1) `REAL300000220110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220110 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 119, 164, 164, 71, 71, 71, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 12, 71, 71, 71, 71, 119, 119, 9, 9, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 71] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 583 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220110 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 71, 71, 27, 71, 71, 71, 137, 170, 170, 1, 2, 2, 2, 3, 3, 12, 12, 71, 71, 71, 71, 170, 170, 170, 170, 170, 170, 170, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 42] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 569 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220110 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220110 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220110/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220110 Building REAL300000220111 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220111' /scratch/stefan/7769890/working/building/REAL300000220111 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220111 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220111/0 /scratch/stefan/7769890/working/building/REAL300000220111 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/111 `/scratch/stefan/7769890/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220111 none CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 60, 56, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 38, 122, 122, 122, 122, 122, 122, 122, 60, 60, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 38, 38, 38] 201 rigid atoms, others: [45, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 460 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220111 none CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 9, 5, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 38, 62, 62, 21, 21, 21, 1, 1, 1, 3, 19, 19, 19, 19, 19, 19, 19, 9, 9, 1, 1, 5, 5, 21, 21, 21, 38, 38, 21, 1, 3, 3, 3] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 46, 25, 23, 24, 4, 37] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 306 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220111 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220111 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220111/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220111 Building REAL300000220112 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220112' /scratch/stefan/7769890/working/building/REAL300000220112 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220112 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220112/0 /scratch/stefan/7769890/working/building/REAL300000220112 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/112 `/scratch/stefan/7769890/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220112 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 87, 80, 30, 30, 30, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 30, 30, 30, 64, 135, 135, 135, 135, 135, 87, 87, 30, 30, 9, 9, 2, 2, 2, 3, 3, 1, 30, 64, 64, 64] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 484 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220112 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 12, 7, 1, 1, 1, 1, 1, 1, 5, 5, 30, 30, 30, 30, 30, 55, 88, 88, 30, 30, 30, 1, 1, 1, 3, 20, 20, 20, 20, 20, 12, 12, 1, 1, 5, 5, 30, 30, 30, 55, 55, 30, 1, 4, 4, 4] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 43, 22, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 407 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220112 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220112 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220112/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220112 Building REAL300000220113 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220113' /scratch/stefan/7769890/working/building/REAL300000220113 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220113 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220113/0 /scratch/stefan/7769890/working/building/REAL300000220113 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/113 `/scratch/stefan/7769890/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220113 none C=CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [143, 129, 41, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 21, 21, 21, 44, 143, 143, 143, 129, 129, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 44, 44, 44] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 568 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220113 none C=CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 15, 3, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 40, 69, 69, 21, 21, 21, 1, 1, 1, 3, 39, 39, 39, 15, 15, 1, 1, 5, 5, 21, 21, 21, 40, 40, 21, 1, 3, 3, 3] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 22, 23, 24, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 379 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220113 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220113 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220113/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220113 Building REAL300000220114 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220114' /scratch/stefan/7769890/working/building/REAL300000220114 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220114 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220114/0 /scratch/stefan/7769890/working/building/REAL300000220114 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/114 `/scratch/stefan/7769890/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)O2)=N1) `REAL300000220114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220114 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [62, 61, 62, 62, 92, 120, 120, 62, 62, 62, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 2, 2, 7, 7, 1, 61, 62, 62, 62, 92, 92, 62, 13, 13, 1, 1, 7, 7, 7, 7] 121 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 396 number of broken/clashed sets: 120 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220114 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 62, 62, 62, 62, 98, 98, 91, 91, 98, 98, 62, 1, 2, 2, 2, 3, 3, 1, 12, 12, 62, 62, 98, 98, 98, 98] 121 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 197 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220114 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 121, 121, 121, 98, 98, 98, 42, 42, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 98, 98, 98, 98, 121, 121, 98, 42, 42, 7, 7, 1, 1, 1, 1] 121 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 306 number of broken/clashed sets: 120 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220114 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220114 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220114/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220114 Building REAL300000220115 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220115' /scratch/stefan/7769890/working/building/REAL300000220115 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220115 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220115/0 /scratch/stefan/7769890/working/building/REAL300000220115 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/115 `/scratch/stefan/7769890/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)O2)=N1) `REAL300000220115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220115 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 94, 101, 101, 66, 66, 66, 12, 12, 1, 1, 1, 1, 1, 1, 10, 10, 1, 10, 10, 10, 1, 66, 66, 66, 66, 94, 94, 66, 12, 12, 1, 1, 10, 10, 2, 10] 201 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 309 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220115 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 13, 13, 66, 66, 66, 66, 166, 166, 95, 166, 166, 166, 66, 1, 2, 2, 2, 3, 3, 1, 13, 13, 66, 66, 166, 166, 151, 166] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 518 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220115 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 166, 201, 201, 201, 166, 166, 166, 63, 63, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 166, 166, 166, 166, 201, 201, 166, 63, 63, 10, 10, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 471 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220115 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220115 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220115/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220115 Building REAL300000220116 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220116' /scratch/stefan/7769890/working/building/REAL300000220116 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220116 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220116/0 /scratch/stefan/7769890/working/building/REAL300000220116 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/116 `/scratch/stefan/7769890/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=C(C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)OC(C)C2) `REAL300000220116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220116 none COC1=CC2=C(C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)OC(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [71, 56, 56, 56, 56, 56, 56, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 56, 56, 56, 56, 71, 71, 71, 56, 56, 11, 11, 3, 3, 2, 2, 2, 1, 56, 56, 56, 56, 56, 56] 91 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 131 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: REAL300000220116 none COC1=CC2=C(C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)OC(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 56, 56, 56, 56, 56, 83, 91, 91, 56, 56, 56, 1, 1, 1, 1, 4, 4, 4, 1, 1, 11, 11, 83, 83, 56, 56, 56, 56, 1, 2, 2, 2, 1, 1] 91 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 39, 44, 43, 22, 23, 24, 25, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 287 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220116 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220116 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220116/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220116 Building REAL300000220117 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220117' /scratch/stefan/7769890/working/building/REAL300000220117 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220117 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220117/0 /scratch/stefan/7769890/working/building/REAL300000220117 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/117 `/scratch/stefan/7769890/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C=C2)N1) `REAL300000220117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220117 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [13, 13, 13, 13, 24, 25, 25, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 13, 13, 13, 13, 24, 24, 3, 3, 1, 1, 4, 3, 1, 1, 13] 26 rigid atoms, others: [32, 33, 36, 37, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38]) total number of confs: 94 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: REAL300000220117 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 9, 9, 25, 25, 25, 25, 13, 13, 1, 2, 2, 2, 3, 3, 9, 9, 13, 13, 25, 25, 13, 13, 1] 26 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 81 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220117 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC=N3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [25, 25, 25, 25, 26, 26, 26, 25, 25, 25, 6, 6, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 25, 25, 25, 25, 26, 26, 6, 6, 4, 4, 1, 1, 4, 4, 25] 26 rigid atoms, others: [34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 26 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220117 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220117 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220117/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220117 Building REAL300000220118 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220118' /scratch/stefan/7769890/working/building/REAL300000220118 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220118 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220118/0 /scratch/stefan/7769890/working/building/REAL300000220118 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/118 `/scratch/stefan/7769890/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)S2)N1) `REAL300000220118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220118 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [51, 51, 51, 51, 63, 63, 63, 51, 51, 51, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 51, 51, 51, 51, 63, 63, 13, 13, 1, 1, 7, 7, 2, 7, 7, 51] 94 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 165 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220118 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 6, 6, 1, 1, 1, 1, 1, 10, 10, 51, 51, 51, 51, 82, 82, 57, 82, 82, 51, 1, 2, 2, 2, 3, 3, 10, 10, 51, 51, 82, 82, 76, 82, 82, 1] 94 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 257 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220118 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [82, 82, 82, 82, 94, 94, 94, 82, 82, 82, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 82, 82, 82, 82, 94, 94, 50, 50, 7, 7, 1, 1, 1, 1, 1, 82] 94 rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 230 number of broken/clashed sets: 93 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220118 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220118 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220118/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220118 Building REAL300000220119 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220119' /scratch/stefan/7769890/working/building/REAL300000220119 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220119 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220119/0 /scratch/stefan/7769890/working/building/REAL300000220119 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/119 `/scratch/stefan/7769890/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN(C3=CC=CC=C3)N=C2)N1) `REAL300000220119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220119 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [32, 32, 32, 32, 49, 49, 49, 32, 32, 32, 12, 12, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 32, 33, 33, 33, 49, 49, 12, 12, 4, 4, 2, 4, 4, 1, 31] 49 rigid atoms, others: [37, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 170 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: REAL300000220119 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 32, 32, 32, 35, 35, 35, 35, 35, 32, 32, 1, 2, 2, 2, 3, 3, 10, 10, 35, 35, 35, 35, 35, 32, 1] 49 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 85 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220119 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [35, 35, 35, 35, 49, 49, 49, 35, 35, 35, 20, 20, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 49, 49, 20, 20, 1, 1, 1, 1, 1, 4, 35] 49 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 153 number of broken/clashed sets: 48 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220119 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220119 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220119/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220119 Building REAL300000220120 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220120' /scratch/stefan/7769890/working/building/REAL300000220120 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220120 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220120/0 /scratch/stefan/7769890/working/building/REAL300000220120 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/120 `/scratch/stefan/7769890/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1) `REAL300000220120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220120 none COC1=CC(OC)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [97, 22, 21, 58, 58, 58, 96, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 58, 58, 93, 58, 97, 97, 97, 58, 96, 96, 96, 12, 12, 3, 3, 2, 2, 2, 1, 93, 93, 93, 58] 185 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 415 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: REAL300000220120 none COC1=CC(OC)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 1, 1, 8, 8, 58, 57, 58, 58, 58, 95, 142, 142, 58, 58, 58, 1, 1, 3, 1, 2, 2, 2, 1, 4, 4, 4, 8, 8, 95, 95, 58, 58, 58, 58, 4, 4, 4, 1] 185 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 44, 22, 23, 25, 29] set([0, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 507 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220120 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220120 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220120/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220120 Building REAL300000220121 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220121' /scratch/stefan/7769890/working/building/REAL300000220121 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220121 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220121/0 /scratch/stefan/7769890/working/building/REAL300000220121 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/121 `/scratch/stefan/7769890/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CCC#N)N=C2C2=CC=CC=C2)N1) `REAL300000220121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220121 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CCC#N)N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.1', 'N.1', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 72, 89, 89, 42, 42, 42, 11, 11, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 1, 6, 6, 2, 6, 6, 42, 43, 43, 43, 72, 72, 11, 11, 1, 6, 6, 10, 10, 6, 6, 5, 6, 6, 42] 201 rigid atoms, others: [36, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 367 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220121 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CCC#N)N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.1', 'N.1', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 42, 42, 42, 111, 140, 140, 42, 42, 42, 65, 65, 57, 65, 65, 1, 2, 2, 2, 3, 3, 9, 9, 42, 111, 111, 140, 140, 65, 65, 64, 65, 65, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 46, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 641 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220121 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CCC#N)N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.1', 'N.1', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 102, 116, 116, 65, 65, 65, 23, 23, 6, 6, 6, 6, 6, 19, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 102, 102, 23, 23, 6, 19, 19, 27, 27, 1, 1, 1, 1, 1, 65] 201 rigid atoms, others: [41, 42, 43, 44, 45, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 477 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220121 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220121 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220121/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220121 Building REAL300000220122 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220122' /scratch/stefan/7769890/working/building/REAL300000220122 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220122 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220122/0 /scratch/stefan/7769890/working/building/REAL300000220122 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/122 `/scratch/stefan/7769890/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCOC3=C2)=N1) `REAL300000220122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220122 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 21, 21, 21, 31, 31, 31, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 31, 31, 21, 6, 6, 1, 1, 1, 1] 31 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 94 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: REAL300000220122 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 9, 9, 21, 21, 21, 21] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 65 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220122 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220122 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220122/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220122 Building REAL300000220123 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220123' /scratch/stefan/7769890/working/building/REAL300000220123 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220123 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220123/0 /scratch/stefan/7769890/working/building/REAL300000220123 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/123 `/scratch/stefan/7769890/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C2O1) `REAL300000220123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220123 none CCCCC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 115, 99, 39, 39, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 117, 117, 117, 117, 117, 115, 115, 99, 99, 9, 9, 3, 3, 1, 1, 1, 1, 39, 39, 39, 39] 201 rigid atoms, others: [43, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 41, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47]) 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: REAL300000220123 none CCCCC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 9, 5, 1, 1, 1, 1, 9, 9, 39, 39, 39, 39, 39, 67, 95, 95, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 11, 11, 10, 10, 5, 5, 9, 9, 67, 67, 39, 39, 39, 39, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220123 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220123 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220123/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220123 Building REAL300000220124 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220124' /scratch/stefan/7769890/working/building/REAL300000220124 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220124 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220124/0 /scratch/stefan/7769890/working/building/REAL300000220124 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/124 `/scratch/stefan/7769890/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC(F)F) `REAL300000220124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220124 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 40, 40, 40, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 40, 40, 40, 40, 92, 145, 145, 86, 86, 86, 40, 11, 11, 2, 2, 2, 3, 3, 1, 40, 40, 145] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 551 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220124 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 40, 40, 40, 40, 40, 67, 104, 104, 40, 40, 40, 1, 1, 1, 1, 5, 20, 20, 4, 4, 4, 1, 5, 5, 40, 40, 40, 67, 67, 40, 1, 1, 20] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 19, 20, 21, 22, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 429 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220124 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220124 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220124/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220124 Building REAL300000220125 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220125' /scratch/stefan/7769890/working/building/REAL300000220125 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220125 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220125/0 /scratch/stefan/7769890/working/building/REAL300000220125 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/125 `/scratch/stefan/7769890/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CN=C3C=C2)N1) `REAL300000220125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220125 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CN=C3C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 27, 27, 27, 18, 18, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 27, 27, 5, 5, 1, 1, 1, 1, 1, 1, 18] 27 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 83 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: REAL300000220125 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CN=C3C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 3, 8, 8, 18, 18, 18, 18, 18, 18, 1] 27 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220125 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220125 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220125/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220125 Building REAL300000220126 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220126' /scratch/stefan/7769890/working/building/REAL300000220126 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220126 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220126/0 /scratch/stefan/7769890/working/building/REAL300000220126 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/126 `/scratch/stefan/7769890/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(C)(C)C)C=C2)N1) `REAL300000220126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220126 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(C)(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 13, 25, 25, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 13] 25 rigid atoms, others: [32, 42, 43, 12, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 76 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: REAL300000220126 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(C)(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 11, 11, 25, 25, 25, 13, 13, 1, 2, 2, 2, 3, 3, 9, 9, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 13, 1] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 44, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 128 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220126 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220126 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220126/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220126 Building REAL300000220127 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220127' /scratch/stefan/7769890/working/building/REAL300000220127 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220127 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220127/0 /scratch/stefan/7769890/working/building/REAL300000220127 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/127 `/scratch/stefan/7769890/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C=C2F)N1) `REAL300000220127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220127 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [28, 28, 28, 28, 38, 38, 38, 28, 28, 28, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 38, 38, 10, 10, 1, 1, 1, 28] 38 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 107 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: REAL300000220127 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 28, 28, 14, 28, 28, 28, 28, 1, 2, 2, 2, 3, 3, 11, 11, 28, 28, 28, 1] 38 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 119 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220127 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220127 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220127/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220127 Building REAL300000220128 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220128' /scratch/stefan/7769890/working/building/REAL300000220128 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220128 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220128/0 /scratch/stefan/7769890/working/building/REAL300000220128 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/128 `/scratch/stefan/7769890/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Cl)=C2Cl)=N1) `REAL300000220128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220128 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Cl)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [27, 27, 27, 27, 35, 35, 35, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 35, 35, 27, 7, 7, 1, 1, 1] 35 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 89 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220128 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Cl)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 1, 11, 11, 27, 27, 27] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 71 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220128 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220128 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220128/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220128 Building REAL300000220129 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220129' /scratch/stefan/7769890/working/building/REAL300000220129 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220129 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220129/0 /scratch/stefan/7769890/working/building/REAL300000220129 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/129 `/scratch/stefan/7769890/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(Cl)=C2)=N1) `REAL300000220129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220129 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 20, 20, 20, 32, 32, 32, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 32, 32, 20, 7, 7, 1, 1, 1] 32 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 106 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: REAL300000220129 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 7, 7, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 1, 8, 8, 20, 20, 20] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 63 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220129 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220129 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220129/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220129 Building REAL300000220130 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220130' /scratch/stefan/7769890/working/building/REAL300000220130 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220130 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220130/0 /scratch/stefan/7769890/working/building/REAL300000220130 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/130 `/scratch/stefan/7769890/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C=C2)=N1) `REAL300000220130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220130 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 49, 78, 78, 28, 28, 28, 4, 4, 1, 1, 1, 1, 1, 1, 13, 43, 43, 1, 1, 28, 28, 28, 28, 49, 49, 28, 4, 4, 1, 1, 43, 1, 1] 187 rigid atoms, others: [32, 33, 35, 36, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 408 number of broken/clashed sets: 187 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220130 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 7, 7, 1, 1, 1, 1, 1, 13, 13, 28, 28, 13, 13, 108, 156, 156, 28, 28, 1, 2, 2, 2, 3, 3, 1, 13, 13, 28, 28, 156, 28, 28] 187 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 479 number of broken/clashed sets: 187 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220130 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220130 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220130/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220130 Building REAL300000220131 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220131' /scratch/stefan/7769890/working/building/REAL300000220131 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220131 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220131/0 /scratch/stefan/7769890/working/building/REAL300000220131 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/131 `/scratch/stefan/7769890/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2C(F)(F)F)=N1) `REAL300000220131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220131 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 28, 35, 35, 35, 28, 28, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 28, 28, 28, 28, 35, 35, 28, 5, 5, 1, 1, 1, 1] 35 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 86 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220131 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 28, 28, 20, 28, 28, 28, 28, 28, 28, 1, 2, 2, 2, 3, 3, 1, 11, 11, 28, 28, 20, 28] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220131 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220131 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220131/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220131 Building REAL300000220132 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220132' /scratch/stefan/7769890/working/building/REAL300000220132 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220132 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220132/0 /scratch/stefan/7769890/working/building/REAL300000220132 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/132 `/scratch/stefan/7769890/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220132 none CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 137, 84, 71, 24, 24, 35, 35, 13, 13, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 35, 35, 142, 142, 142, 142, 142, 137, 137, 84, 84, 35, 35, 13, 13, 2, 2, 2, 3, 3, 1, 35, 35] 201 rigid atoms, others: [43, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 551 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220132 none CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 4, 1, 1, 1, 1, 1, 1, 5, 5, 35, 35, 35, 35, 35, 63, 98, 98, 35, 35, 35, 1, 1, 20, 20, 20, 20, 20, 16, 16, 6, 6, 1, 1, 5, 5, 35, 35, 35, 63, 63, 35, 1, 1] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 44, 45, 23, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 430 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220132 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220132 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220132/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220132 Building REAL300000220133 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220133' /scratch/stefan/7769890/working/building/REAL300000220133 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220133 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220133/0 /scratch/stefan/7769890/working/building/REAL300000220133 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/133 `/scratch/stefan/7769890/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCCC(C)C)C=C2)=N1) `REAL300000220133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220133 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCCC(C)C)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 33, 54, 54, 19, 19, 19, 4, 4, 1, 1, 1, 1, 1, 1, 7, 11, 21, 25, 25, 1, 1, 19, 19, 19, 19, 33, 33, 19, 4, 4, 1, 1, 11, 11, 21, 21, 25, 25, 25, 25, 25, 25, 25, 1, 1] 201 rigid atoms, others: [48, 34, 35, 12, 13, 14, 15, 16, 17, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 308 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220133 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCCC(C)C)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 19, 19, 12, 12, 69, 76, 106, 129, 129, 19, 19, 1, 2, 2, 2, 3, 3, 1, 12, 12, 19, 19, 76, 76, 106, 106, 129, 129, 129, 129, 129, 129, 129, 19, 19] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 513 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220133 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220133 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220133/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220133 Building REAL300000220134 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220134' /scratch/stefan/7769890/working/building/REAL300000220134 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220134 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220134/0 /scratch/stefan/7769890/working/building/REAL300000220134 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/134 `/scratch/stefan/7769890/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220134 none CCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 126, 126, 126, 54, 54, 13, 13, 21, 21, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 54, 54, 21, 21, 9, 9, 2, 2, 2, 3, 3, 1, 21, 21] 201 rigid atoms, others: [49, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51]) total number of confs: 481 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220134 none CCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 36, 56, 56, 21, 21, 21, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 1, 5, 5, 21, 21, 21, 36, 36, 21, 1, 1] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 40, 50, 51, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 232 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220134 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220134 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220134/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220134 Building REAL300000220135 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220135' /scratch/stefan/7769890/working/building/REAL300000220135 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220135 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220135/0 /scratch/stefan/7769890/working/building/REAL300000220135 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/135 `/scratch/stefan/7769890/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC3=CC=CC=C3)=C2)N1) `REAL300000220135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220135 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC3=CC=CC=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 39, 44, 44, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 9, 14, 14, 10, 14, 14, 1, 22, 22, 22, 22, 39, 39, 5, 5, 1, 1, 1, 14, 14, 14, 14, 14, 1, 22] 201 rigid atoms, others: [34, 35, 36, 42, 12, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 43]) total number of confs: 188 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220135 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC3=CC=CC=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 104, 120, 120, 119, 120, 120, 22, 1, 2, 2, 2, 3, 3, 7, 7, 22, 22, 22, 120, 120, 120, 120, 120, 22, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 43, 26] set([4, 5, 6, 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, 41, 42]) total number of confs: 199 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220135 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC3=CC=CC=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 201, 201, 201, 120, 120, 120, 42, 42, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 14, 120, 120, 120, 120, 201, 201, 42, 42, 14, 14, 14, 1, 1, 1, 1, 1, 14, 120] 201 rigid atoms, others: [37, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43]) total number of confs: 690 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220135 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220135 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220135/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220135 Building REAL300000220136 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220136' /scratch/stefan/7769890/working/building/REAL300000220136 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220136 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220136/0 /scratch/stefan/7769890/working/building/REAL300000220136 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/136 `/scratch/stefan/7769890/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(OCCC)=C1) `REAL300000220136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220136 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(OCCC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 12, 9, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 12, 12, 20, 27, 52, 12, 61, 61, 61, 61, 61, 35, 35, 12, 12, 7, 7, 2, 2, 2, 3, 3, 1, 27, 27, 53, 53, 53, 53, 53, 12] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 389 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220136 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(OCCC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 17, 27, 27, 12, 12, 12, 1, 1, 5, 12, 23, 1, 14, 14, 14, 14, 14, 6, 6, 1, 1, 6, 6, 12, 12, 12, 17, 17, 12, 12, 12, 24, 24, 24, 24, 24, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 3, 52, 22, 23, 36, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 225 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220136 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220136 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220136/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220136 Building REAL300000220137 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220137' /scratch/stefan/7769890/working/building/REAL300000220137 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220137 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220137/0 /scratch/stefan/7769890/working/building/REAL300000220137 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/137 `/scratch/stefan/7769890/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(=O)[O-])C=C2)N1) `REAL300000220137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220137 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 13, 13, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 13] 13 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 25 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: REAL300000220137 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 9, 11, 13, 13, 13, 13, 1, 2, 2, 2, 3, 3, 9, 9, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220137 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220137 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220137/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220137 Building REAL300000220138 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220138' /scratch/stefan/7769890/working/building/REAL300000220138 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220138 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220138/0 /scratch/stefan/7769890/working/building/REAL300000220138 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/138 `/scratch/stefan/7769890/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2I)=N1) `REAL300000220138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220138 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2I)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [27, 27, 27, 27, 35, 35, 35, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 35, 35, 27, 7, 7, 1, 1, 1, 1] 35 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 89 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220138 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2I)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 27, 27, 13, 27, 27, 27, 1, 2, 2, 2, 3, 3, 1, 11, 11, 27, 27, 25, 27] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 124 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220138 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220138 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220138/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220138 Building REAL300000220139 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220139' /scratch/stefan/7769890/working/building/REAL300000220139 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220139 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220139/0 /scratch/stefan/7769890/working/building/REAL300000220139 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/139 `/scratch/stefan/7769890/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220139 none COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [33, 21, 21, 21, 21, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 33, 33, 33, 21, 21, 21, 10, 10, 3, 3, 2, 2, 2, 1, 21] 61 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 84 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: REAL300000220139 none COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 38, 46, 46, 21, 21, 21, 1, 3, 3, 3, 1, 1, 1, 6, 6, 38, 38, 21, 21, 21, 21, 1] 61 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 25, 26, 27, 36] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220139 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220139 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220139/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220139 Building REAL300000220140 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220140' /scratch/stefan/7769890/working/building/REAL300000220140 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220140 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220140/0 /scratch/stefan/7769890/working/building/REAL300000220140 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/140 `/scratch/stefan/7769890/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220140 none CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 128, 35, 35, 35, 35, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 35, 35, 35, 79, 151, 151, 151, 151, 151, 35, 35, 10, 10, 2, 2, 2, 3, 3, 1, 35, 79, 79, 79] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 405 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220140 none CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 9, 1, 1, 1, 1, 1, 1, 5, 5, 35, 35, 35, 35, 35, 62, 107, 107, 35, 35, 35, 1, 1, 1, 3, 26, 26, 26, 26, 26, 1, 1, 5, 5, 35, 35, 35, 62, 62, 35, 1, 4, 4, 4] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 469 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220140 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220140 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220140/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220140 Building REAL300000220141 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220141' /scratch/stefan/7769890/working/building/REAL300000220141 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220141 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220141/0 /scratch/stefan/7769890/working/building/REAL300000220141 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/141 `/scratch/stefan/7769890/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(C)C)C=C2)N1) `REAL300000220141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220141 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 14, 14, 26, 34, 34, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 14, 14, 14, 14, 26, 26, 3, 3, 1, 1, 4, 5, 5, 5, 5, 5, 5, 1, 1, 14] 41 rigid atoms, others: [39, 40, 12, 13, 14, 15, 16, 17, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 148 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: REAL300000220141 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 14, 14, 9, 9, 36, 36, 14, 14, 1, 2, 2, 2, 3, 3, 9, 9, 14, 14, 36, 36, 36, 36, 36, 36, 36, 14, 14, 1] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 41] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220141 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220141 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220141/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220141 Building REAL300000220142 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220142' /scratch/stefan/7769890/working/building/REAL300000220142 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220142 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220142/0 /scratch/stefan/7769890/working/building/REAL300000220142 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/142 `/scratch/stefan/7769890/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC) `REAL300000220142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220142 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 91, 54, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 46, 46, 146, 146, 146, 146, 146, 91, 91, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 46, 46, 46, 46, 46] 201 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49]) total number of confs: 635 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220142 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 38, 68, 68, 21, 21, 21, 1, 1, 1, 5, 5, 26, 26, 26, 26, 26, 13, 13, 1, 1, 5, 5, 21, 21, 21, 38, 38, 21, 1, 5, 5, 5, 5, 5] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 44, 35, 22, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 365 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220142 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220142 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220142/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220142 Building REAL300000220143 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220143' /scratch/stefan/7769890/working/building/REAL300000220143 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220143 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220143/0 /scratch/stefan/7769890/working/building/REAL300000220143 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/143 `/scratch/stefan/7769890/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1[N+](=O)[O-]) `REAL300000220143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220143 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 3, 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: [14, 14, 21, 21, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 3, 3, 2, 2, 2, 1, 21] 31 rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 117 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: REAL300000220143 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 3, 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, 5, 5, 21, 21, 21, 21, 21, 31, 31, 31, 21, 21, 21, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 5, 5, 31, 31, 21, 21, 21, 21, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 27, 28, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 102 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220143 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220143 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220143/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220143 Building REAL300000220144 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220144' /scratch/stefan/7769890/working/building/REAL300000220144 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220144 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220144/0 /scratch/stefan/7769890/working/building/REAL300000220144 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/144 `/scratch/stefan/7769890/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([O-])C([N+](=O)[O-])=C2)N1) `REAL300000220144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220144 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([O-])C([N+](=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 33, 33, 33, 26, 26, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 26, 26, 26, 26, 33, 33, 6, 6, 1, 1, 1, 26] 33 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 84 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220144 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([O-])C([N+](=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 26, 26, 9, 9, 26, 26, 26, 26, 26, 1, 2, 2, 2, 3, 3, 9, 9, 26, 26, 26, 1] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 97 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220144 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220144 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220144/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220144 Building REAL300000220145 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220145' /scratch/stefan/7769890/working/building/REAL300000220145 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220145 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220145/0 /scratch/stefan/7769890/working/building/REAL300000220145 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/145 `/scratch/stefan/7769890/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3C=C2)N1) `REAL300000220145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220145 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [18, 18, 18, 18, 27, 27, 27, 18, 18, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 27, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 18] 27 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 83 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: REAL300000220145 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 3, 8, 8, 18, 18, 18, 18, 18, 18, 18, 1] 27 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220145 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220145 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220145/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220145 Building REAL300000220146 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220146' /scratch/stefan/7769890/working/building/REAL300000220146 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220146 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220146/0 /scratch/stefan/7769890/working/building/REAL300000220146 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/146 `/scratch/stefan/7769890/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=CC=C1) `REAL300000220146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220146 none COC1=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [55, 40, 40, 40, 40, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 40, 40, 40, 40, 40, 55, 55, 55, 11, 11, 3, 3, 2, 2, 2, 1, 40, 40, 40, 40] 81 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) 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: REAL300000220146 none COC1=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 13, 13, 39, 39, 40, 40, 40, 59, 81, 81, 40, 40, 40, 1, 1, 1, 1, 1, 3, 3, 3, 13, 13, 59, 59, 40, 40, 40, 40, 1, 1, 1, 1] 81 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 20, 21, 22, 23, 24, 36, 38, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220146 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220146 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220146/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220146 Building REAL300000220147 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220147' /scratch/stefan/7769890/working/building/REAL300000220147 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220147 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220147/0 /scratch/stefan/7769890/working/building/REAL300000220147 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/147 `/scratch/stefan/7769890/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(C)C)C([N+](=O)[O-])=C2)=N1) `REAL300000220147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220147 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(C)C)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [23, 23, 23, 23, 33, 33, 33, 23, 23, 23, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 23, 23, 23, 23, 33, 33, 23, 6, 6, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1] 33 rigid atoms, others: [34, 35, 43, 12, 13, 14, 15, 16, 17, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 105 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220147 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(C)C)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 23, 23, 11, 15, 23, 23, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 3, 1, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 138 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220147 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220147 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220147/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220147 Building REAL300000220148 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220148' /scratch/stefan/7769890/working/building/REAL300000220148 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220148 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220148/0 /scratch/stefan/7769890/working/building/REAL300000220148 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/148 `/scratch/stefan/7769890/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=CC=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220148 none CC1=NN(CC2=CC=CC=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 39, 39, 140, 140, 140, 140, 140, 201, 201, 201, 140, 140, 140, 10, 10, 10, 3, 3, 1, 1, 1, 1, 1, 10, 10, 10, 39, 39, 140, 140, 140, 201, 201, 140] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 603 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220148 none CC1=NN(CC2=CC=CC=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 9, 10, 8, 10, 9, 1, 1, 1, 1, 7, 7, 47, 47, 47, 47, 47, 82, 93, 93, 47, 47, 47, 2, 2, 2, 5, 5, 9, 10, 10, 10, 9, 2, 2, 2, 7, 7, 47, 47, 47, 82, 82, 47] 201 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 363 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220148 none CC1=NN(CC2=CC=CC=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 128, 140, 140, 132, 140, 140, 47, 47, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 47, 47, 47, 128, 128, 140, 140, 140, 140, 140, 47, 47, 47, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 523 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220148 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220148 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220148/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220148 Building REAL300000220149 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220149' /scratch/stefan/7769890/working/building/REAL300000220149 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220149 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220149/0 /scratch/stefan/7769890/working/building/REAL300000220149 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/149 `/scratch/stefan/7769890/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(C)C) `REAL300000220149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220149 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 57, 24, 24, 24, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 24, 24, 24, 24, 107, 134, 161, 163, 58, 58, 58, 58, 58, 24, 8, 8, 2, 2, 2, 3, 3, 1, 24, 24, 134, 134, 163, 163, 163, 163, 163, 163, 163] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 560 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220149 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 5, 5, 24, 24, 24, 24, 24, 42, 75, 75, 24, 24, 24, 1, 1, 1, 1, 9, 17, 25, 28, 6, 6, 6, 6, 6, 1, 5, 5, 24, 24, 24, 42, 42, 24, 1, 1, 17, 17, 28, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 42, 43, 20, 21, 22, 23] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 413 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220149 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220149 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220149/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220149 Building REAL300000220150 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220150' /scratch/stefan/7769890/working/building/REAL300000220150 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220150 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220150/0 /scratch/stefan/7769890/working/building/REAL300000220150 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/150 `/scratch/stefan/7769890/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CC=C2F)=N1) `REAL300000220150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220150 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [37, 37, 37, 37, 49, 49, 49, 37, 37, 37, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 49, 49, 37, 11, 11, 1, 1, 1] 49 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 130 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: REAL300000220150 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 37, 37, 37, 31, 37, 37, 37, 1, 2, 2, 2, 3, 3, 1, 9, 9, 37, 37, 37] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 103 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220150 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220150 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220150/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220150 Building REAL300000220151 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220151' /scratch/stefan/7769890/working/building/REAL300000220151 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220151 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220151/0 /scratch/stefan/7769890/working/building/REAL300000220151 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/151 `/scratch/stefan/7769890/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C([N+](=O)[O-])C=C1OC) `REAL300000220151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220151 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C([N+](=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 11, 11, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [88, 39, 39, 39, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 84, 88, 88, 88, 39, 11, 11, 2, 2, 2, 3, 3, 1, 39, 84, 84, 84] 135 rigid atoms, others: [38, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 237 number of broken/clashed sets: 134 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220151 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C([N+](=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 11, 11, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 7, 7, 39, 39, 39, 39, 39, 65, 107, 107, 39, 39, 39, 1, 1, 2, 2, 1, 1, 1, 3, 4, 4, 4, 1, 7, 7, 39, 39, 39, 65, 65, 39, 1, 4, 4, 4] 135 rigid atoms, others: [1, 2, 3, 4, 5, 39, 19, 20, 23, 24, 25, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 394 number of broken/clashed sets: 134 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220151 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220151 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220151/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220151 Building REAL300000220152 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220152' /scratch/stefan/7769890/working/building/REAL300000220152 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220152 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220152/0 /scratch/stefan/7769890/working/building/REAL300000220152 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/152 `/scratch/stefan/7769890/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2F)=N1) `REAL300000220152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220152 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [19, 19, 19, 19, 33, 33, 33, 19, 19, 19, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 33, 33, 19, 9, 9, 1, 1, 1] 33 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 119 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220152 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 19, 19, 15, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 1, 9, 9, 19, 19, 19] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220152 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220152 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220152/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220152 Building REAL300000220153 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220153' /scratch/stefan/7769890/working/building/REAL300000220153 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220153 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220153/0 /scratch/stefan/7769890/working/building/REAL300000220153 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/153 `/scratch/stefan/7769890/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC([N+](=O)[O-])=C1O) `REAL300000220153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220153 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC([N+](=O)[O-])=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [57, 35, 35, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 57, 57, 57, 35, 11, 11, 2, 2, 2, 3, 3, 1, 35, 70] 140 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 190 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220153 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC([N+](=O)[O-])=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 35, 35, 35, 35, 35, 56, 70, 70, 35, 35, 35, 1, 1, 1, 2, 2, 1, 1, 4, 4, 4, 1, 5, 5, 35, 35, 35, 56, 56, 35, 1, 2] 140 rigid atoms, others: [1, 2, 3, 4, 5, 38, 19, 20, 21, 24, 25, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 242 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220153 /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `1' /scratch/stefan/7769890/working/building/REAL300000220153/1 /scratch/stefan/7769890/working/building/REAL300000220153 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 1 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/154 `/scratch/stefan/7769890/working/3D/154' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC([N+](=O)[O-])=C1[O-]) `REAL300000220153.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220153/1/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: REAL300000220153 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC([N+](=O)[O-])=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [53, 29, 29, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 53, 53, 53, 29, 11, 11, 2, 2, 2, 3, 3, 1, 29] 71 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 117 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220153 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC([N+](=O)[O-])=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 47, 71, 71, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 5, 5, 29, 29, 29, 47, 47, 29, 1] 71 rigid atoms, others: [1, 2, 3, 4, 5, 38, 19, 20, 21, 22, 23, 24, 25, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 247 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220153 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220153 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 1: /scratch/stefan/7769890/working/building/REAL300000220153/1.* 0: /scratch/stefan/7769890/working/building/REAL300000220153/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220153 Building REAL300000220154 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220154' /scratch/stefan/7769890/working/building/REAL300000220154 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220154 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220154/0 /scratch/stefan/7769890/working/building/REAL300000220154 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/155 `/scratch/stefan/7769890/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1) `REAL300000220154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220154 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [27, 15, 15, 15, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 15, 15, 15, 27, 9, 27, 27, 27, 15, 9, 9, 3, 3, 2, 2, 2, 1, 15, 27, 27, 27, 13] 67 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 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: 125 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: REAL300000220154 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 3, 15, 15, 15, 15, 15, 27, 39, 39, 15, 15, 15, 1, 1, 1, 3, 1, 3, 3, 3, 1, 3, 3, 27, 27, 15, 15, 15, 15, 1, 3, 3, 3, 1] 67 rigid atoms, others: [1, 2, 3, 4, 5, 40, 19, 20, 21, 23, 36, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220154 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220154 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220154/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220154 Building REAL300000220155 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220155' /scratch/stefan/7769890/working/building/REAL300000220155 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220155 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220155/0 /scratch/stefan/7769890/working/building/REAL300000220155 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/156 `/scratch/stefan/7769890/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2Br)OCO3)=N1) `REAL300000220155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220155 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2Br)OCO3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'O.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 12, 5, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 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, 19, 31, 31, 31, 19, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 31, 31, 19, 7, 7, 1, 1, 1, 1] 31 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 103 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: REAL300000220155 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2Br)OCO3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'O.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 12, 5, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 1, 11, 11, 19, 19, 19, 19] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 62 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220155 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220155 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220155/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220155 Building REAL300000220156 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220156' /scratch/stefan/7769890/working/building/REAL300000220156 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220156 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220156/0 /scratch/stefan/7769890/working/building/REAL300000220156 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/157 `/scratch/stefan/7769890/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C2C=C1) `REAL300000220156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220156 none COC1=CC2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [33, 17, 17, 17, 17, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 17, 17, 17, 17, 33, 33, 33, 17, 17, 17, 5, 5, 3, 3, 1, 1, 1, 1, 17, 17, 17] 55 rigid atoms, others: [36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42]) total number of confs: 77 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: REAL300000220156 none COC1=CC2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 33, 55, 55, 17, 17, 17, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 5, 5, 33, 33, 17, 17, 17, 17, 1, 1, 1] 55 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 41, 42, 40, 22, 23, 24, 25, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220156 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220156 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220156/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220156 Building REAL300000220157 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220157' /scratch/stefan/7769890/working/building/REAL300000220157 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220157 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220157/0 /scratch/stefan/7769890/working/building/REAL300000220157 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/158 `/scratch/stefan/7769890/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CS2)=N1) `REAL300000220157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220157 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [26, 26, 26, 26, 39, 39, 39, 26, 26, 26, 12, 12, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 39, 39, 26, 12, 12, 1, 1] 39 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 124 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: REAL300000220157 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 26, 26, 26, 26, 26, 1, 2, 2, 2, 3, 3, 1, 11, 11, 26, 26] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 67 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220157 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220157 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220157/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220157 Building REAL300000220158 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220158' /scratch/stefan/7769890/working/building/REAL300000220158 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220158 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220158/0 /scratch/stefan/7769890/working/building/REAL300000220158 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/159 `/scratch/stefan/7769890/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(=O)[O-])C=C2)=N1) `REAL300000220158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220158 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 38, 65, 65, 24, 24, 24, 4, 4, 1, 1, 1, 1, 1, 1, 7, 27, 43, 43, 1, 1, 24, 24, 24, 24, 38, 38, 24, 4, 4, 1, 1, 27, 27, 1, 1] 201 rigid atoms, others: [33, 34, 37, 38, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 355 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220158 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 13, 13, 24, 24, 13, 13, 77, 161, 167, 167, 24, 24, 1, 2, 2, 2, 3, 3, 1, 13, 13, 24, 24, 161, 161, 24, 24] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 580 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220158 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220158 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220158/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220158 Building REAL300000220159 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220159' /scratch/stefan/7769890/working/building/REAL300000220159 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220159 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220159/0 /scratch/stefan/7769890/working/building/REAL300000220159 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/160 `/scratch/stefan/7769890/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(C)=C1O) `REAL300000220159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220159 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(C)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 9, 9, 9, 5, 5, 9, 9, 9, 9, 5, 5, 3, 3, 2, 2, 2, 1, 9, 9, 9, 9, 18] 30 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 69 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: REAL300000220159 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(C)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 5, 5, 10, 10, 10, 10, 10, 15, 15, 15, 10, 10, 10, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 15, 15, 10, 10, 10, 10, 1, 2, 2, 2, 2] 30 rigid atoms, others: [0, 1, 2, 3, 4, 35, 18, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 63 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220159 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220159 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220159/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220159 Building REAL300000220160 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220160' /scratch/stefan/7769890/working/building/REAL300000220160 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220160 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220160/0 /scratch/stefan/7769890/working/building/REAL300000220160 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/161 `/scratch/stefan/7769890/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C([N+](=O)[O-])=C2)=N1) `REAL300000220160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220160 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 41, 41, 41, 23, 23, 23, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 2, 2, 1, 23, 23, 23, 23, 41, 41, 23, 6, 6, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1] 41 rigid atoms, others: [37, 38, 49, 12, 13, 14, 15, 16, 17, 23, 24, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 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: REAL300000220160 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 3, 5, 5, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 29, 29, 29, 29, 29, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 3, 1, 7, 7, 23, 23, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 23] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 72 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220160 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 41, 41, 41, 29, 29, 29, 12, 12, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 3, 29, 29, 29, 29, 41, 41, 29, 12, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3] 41 rigid atoms, others: [48, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49]) total number of confs: 129 number of broken/clashed sets: 41 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220160 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220160 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220160/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220160 Building REAL300000220161 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220161' /scratch/stefan/7769890/working/building/REAL300000220161 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220161 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220161/0 /scratch/stefan/7769890/working/building/REAL300000220161 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/162 `/scratch/stefan/7769890/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1O) `REAL300000220161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220161 none COC1=CC(Br)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [60, 40, 40, 40, 40, 40, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 40, 40, 40, 60, 60, 60, 40, 12, 12, 2, 2, 2, 3, 3, 1, 40, 80] 154 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 209 number of broken/clashed sets: 154 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220161 none COC1=CC(Br)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 40, 40, 40, 40, 40, 66, 77, 77, 40, 40, 40, 1, 1, 1, 3, 3, 3, 1, 10, 10, 40, 40, 40, 66, 66, 40, 1, 2] 154 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 263 number of broken/clashed sets: 154 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220161 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220161 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220161/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220161 Building REAL300000220162 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220162' /scratch/stefan/7769890/working/building/REAL300000220162 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220162 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220162/0 /scratch/stefan/7769890/working/building/REAL300000220162 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/163 `/scratch/stefan/7769890/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220162 none CCCOC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 108, 67, 11, 18, 41, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 41, 41, 160, 160, 160, 160, 160, 108, 108, 41, 41, 11, 11, 3, 3, 1, 1, 1, 1, 41, 41] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 693 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: REAL300000220162 none CCCOC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 4, 1, 1, 1, 1, 1, 1, 6, 6, 41, 41, 41, 41, 41, 68, 106, 106, 41, 41, 41, 1, 1, 21, 21, 21, 21, 21, 12, 12, 1, 1, 6, 6, 68, 68, 41, 41, 41, 41, 1, 1] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 42, 22, 23, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 461 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220162 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220162 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220162/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220162 Building REAL300000220163 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220163' /scratch/stefan/7769890/working/building/REAL300000220163 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220163 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220163/0 /scratch/stefan/7769890/working/building/REAL300000220163 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/164 `/scratch/stefan/7769890/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220163 none CC1=NN(CC2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 29, 29, 152, 152, 152, 152, 152, 201, 201, 201, 152, 152, 152, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 29, 29, 152, 152, 152, 201, 201, 152] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 522 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220163 none CC1=NN(CC2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 7, 8, 7, 8, 7, 1, 1, 1, 1, 7, 7, 45, 45, 45, 45, 45, 85, 106, 106, 45, 45, 45, 2, 2, 2, 5, 5, 7, 8, 8, 8, 7, 7, 7, 45, 45, 45, 85, 85, 45] 201 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 414 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220163 none CC1=NN(CC2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 129, 152, 152, 142, 152, 152, 45, 45, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 45, 45, 45, 129, 129, 152, 152, 152, 152, 152, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [45, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 563 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220163 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220163 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220163/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220163 Building REAL300000220164 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220164' /scratch/stefan/7769890/working/building/REAL300000220164 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220164 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220164/0 /scratch/stefan/7769890/working/building/REAL300000220164 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/165 `/scratch/stefan/7769890/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC#N) `REAL300000220164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220164 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 33, 33, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 33, 33, 33, 33, 79, 139, 139, 77, 77, 77, 33, 9, 9, 2, 2, 2, 3, 3, 1, 33, 33, 139, 139] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 538 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220164 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 33, 33, 33, 33, 33, 59, 98, 98, 33, 33, 33, 1, 1, 1, 1, 5, 18, 18, 4, 4, 4, 1, 5, 5, 33, 33, 33, 59, 59, 33, 1, 1, 18, 18] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 19, 20, 21, 22, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 418 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220164 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220164 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220164/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220164 Building REAL300000220165 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220165' /scratch/stefan/7769890/working/building/REAL300000220165 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220165 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220165/0 /scratch/stefan/7769890/working/building/REAL300000220165 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/166 `/scratch/stefan/7769890/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC) `REAL300000220165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220165 none CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 60, 47, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 43, 43, 134, 134, 134, 134, 134, 134, 134, 60, 60, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 43, 43, 43, 43, 43] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 553 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220165 none CCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 39, 50, 50, 21, 21, 21, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 21, 21, 10, 10, 1, 1, 5, 5, 21, 21, 21, 39, 39, 21, 1, 5, 5, 5, 5, 5] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 47, 23, 24, 25, 38, 5] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52]) total number of confs: 268 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220165 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220165 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220165/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220165 Building REAL300000220166 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220166' /scratch/stefan/7769890/working/building/REAL300000220166 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220166 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220166/0 /scratch/stefan/7769890/working/building/REAL300000220166 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/167 `/scratch/stefan/7769890/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220166 none CC1=NN(C2=CC=CC=C2)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 23, 23, 69, 69, 69, 69, 69, 94, 94, 94, 69, 69, 69, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 94, 94, 69, 69, 69, 69] 94 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 258 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: REAL300000220166 none CC1=NN(C2=CC=CC=C2)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 1, 1, 9, 9, 50, 49, 50, 50, 50, 70, 94, 94, 50, 50, 50, 2, 2, 2, 7, 7, 1, 7, 7, 2, 2, 2, 9, 9, 70, 70, 50, 50, 50, 50] 94 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 314 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220166 none CC1=NN(C2=CC=CC=C2)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 69, 69, 50, 69, 69, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 50, 50, 50, 69, 69, 50, 69, 69, 50, 50, 50, 12, 12, 3, 3, 2, 2, 2, 1] 94 rigid atoms, others: [45, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 190 number of broken/clashed sets: 13 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220166 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220166 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220166/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220166 Building REAL300000220167 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220167' /scratch/stefan/7769890/working/building/REAL300000220167 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220167 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220167/0 /scratch/stefan/7769890/working/building/REAL300000220167 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/168 `/scratch/stefan/7769890/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1OC(F)F) `REAL300000220167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220167 none COC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 54, 54, 54, 54, 54, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 54, 54, 112, 175, 175, 96, 96, 96, 54, 54, 54, 11, 11, 2, 2, 2, 3, 3, 1, 175] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 594 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220167 none COC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 54, 54, 54, 54, 54, 86, 124, 124, 54, 54, 54, 1, 1, 7, 32, 32, 4, 4, 4, 1, 1, 1, 9, 9, 54, 54, 54, 86, 86, 54, 32] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 515 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220167 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220167 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220167/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220167 Building REAL300000220168 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220168' /scratch/stefan/7769890/working/building/REAL300000220168 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220168 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220168/0 /scratch/stefan/7769890/working/building/REAL300000220168 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/169 `/scratch/stefan/7769890/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(C(F)(F)F)=C2)=N1) `REAL300000220168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220168 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 24, 24, 24, 33, 33, 33, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 24, 24, 24, 24, 33, 33, 24, 5, 5, 1, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 94 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220168 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 24, 24, 17, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 3, 1, 9, 9, 24, 24, 23, 24] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 98 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220168 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220168 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220168/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220168 Building REAL300000220169 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220169' /scratch/stefan/7769890/working/building/REAL300000220169 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220169 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220169/0 /scratch/stefan/7769890/working/building/REAL300000220169 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/170 `/scratch/stefan/7769890/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1OC) `REAL300000220169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220169 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 46, 46, 46, 46, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 46, 46, 78, 46, 46, 141, 98, 98, 98, 46, 46, 12, 12, 3, 3, 2, 2, 2, 1, 78, 78, 78, 141, 141, 141] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 364 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: REAL300000220169 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(OC)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 46, 46, 46, 46, 46, 79, 119, 119, 46, 46, 46, 1, 1, 4, 1, 1, 6, 4, 4, 4, 1, 1, 9, 9, 79, 79, 46, 46, 46, 46, 5, 5, 5, 7, 7, 7] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 23, 24, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 453 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220169 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220169 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220169/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220169 Building REAL300000220170 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220170' /scratch/stefan/7769890/working/building/REAL300000220170 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220170 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220170/0 /scratch/stefan/7769890/working/building/REAL300000220170 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/171 `/scratch/stefan/7769890/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220170 none CCOC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 121, 59, 59, 59, 30, 59, 59, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 164, 164, 164, 164, 164, 59, 59, 59, 59, 13, 12, 3, 3, 2, 2, 2, 1] 201 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 557 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: REAL300000220170 none CCOC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 59, 59, 59, 59, 59, 92, 137, 137, 59, 59, 59, 25, 25, 25, 25, 25, 1, 1, 1, 1, 9, 9, 92, 92, 59, 59, 59, 59] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 526 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220170 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220170 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220170/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220170 Building REAL300000220171 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220171' /scratch/stefan/7769890/working/building/REAL300000220171 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220171 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220171/0 /scratch/stefan/7769890/working/building/REAL300000220171 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/172 `/scratch/stefan/7769890/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220171 none CCOC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [83, 54, 22, 22, 35, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 35, 35, 83, 83, 83, 83, 83, 35, 35, 11, 11, 3, 3, 2, 2, 2, 1, 35, 35] 107 rigid atoms, others: [37, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 340 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: REAL300000220171 none CCOC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [9, 3, 1, 1, 1, 1, 1, 1, 6, 6, 35, 35, 35, 35, 35, 57, 85, 85, 35, 35, 35, 1, 1, 9, 9, 9, 9, 9, 1, 1, 6, 6, 57, 57, 35, 35, 35, 35, 1, 1] 107 rigid atoms, others: [2, 3, 4, 5, 6, 7, 39, 21, 22, 38, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 318 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220171 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220171 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220171/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220171 Building REAL300000220172 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220172' /scratch/stefan/7769890/working/building/REAL300000220172 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220172 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220172/0 /scratch/stefan/7769890/working/building/REAL300000220172 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/173 `/scratch/stefan/7769890/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220172 none COC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [75, 61, 61, 61, 28, 61, 61, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 75, 75, 75, 61, 61, 61, 61, 12, 11, 3, 3, 2, 2, 2, 1] 95 rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 258 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: REAL300000220172 none COC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 61, 61, 61, 61, 61, 89, 95, 95, 61, 61, 61, 4, 4, 4, 1, 1, 1, 1, 12, 12, 89, 89, 61, 61, 61, 61] 95 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 286 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220172 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220172 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220172/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220172 Building REAL300000220173 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220173' /scratch/stefan/7769890/working/building/REAL300000220173 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220173 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220173/0 /scratch/stefan/7769890/working/building/REAL300000220173 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/174 `/scratch/stefan/7769890/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3)C=C2)=N1) `REAL300000220173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220173 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 41, 64, 64, 25, 25, 25, 4, 4, 1, 1, 1, 1, 1, 1, 3, 11, 23, 23, 11, 23, 23, 1, 1, 25, 25, 25, 25, 41, 41, 25, 4, 4, 1, 1, 11, 11, 23, 23, 11, 23, 23, 1, 1] 201 rigid atoms, others: [45, 36, 37, 12, 13, 14, 15, 16, 17, 46, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 296 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220173 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 13, 13, 25, 25, 13, 13, 42, 103, 155, 155, 103, 155, 155, 25, 25, 1, 2, 2, 2, 3, 3, 1, 13, 13, 25, 25, 103, 103, 155, 155, 103, 155, 155, 25, 25] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 632 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220173 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 155, 155, 155, 201, 201, 201, 155, 155, 155, 47, 47, 22, 22, 23, 23, 11, 3, 1, 1, 1, 1, 1, 1, 1, 23, 23, 155, 155, 155, 155, 201, 201, 155, 47, 47, 23, 23, 3, 3, 1, 1, 1, 1, 1, 23, 23] 201 rigid atoms, others: [40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46]) total number of confs: 564 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220173 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220173 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220173/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220173 Building REAL300000220174 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220174' /scratch/stefan/7769890/working/building/REAL300000220174 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220174 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220174/0 /scratch/stefan/7769890/working/building/REAL300000220174 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/175 `/scratch/stefan/7769890/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220174 none COC1=CC=C(Br)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [81, 67, 67, 67, 17, 67, 67, 67, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 81, 81, 81, 67, 67, 67, 11, 11, 2, 2, 2, 3, 3, 1] 103 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 290 number of broken/clashed sets: 103 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220174 none COC1=CC=C(Br)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 67, 67, 67, 67, 67, 97, 103, 103, 67, 67, 67, 4, 4, 4, 1, 1, 1, 11, 11, 67, 67, 67, 97, 97, 67] 103 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 302 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220174 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220174 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220174/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220174 Building REAL300000220175 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220175' /scratch/stefan/7769890/working/building/REAL300000220175 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220175 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220175/0 /scratch/stefan/7769890/working/building/REAL300000220175 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/176 `/scratch/stefan/7769890/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Br)=C1O) `REAL300000220175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220175 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [57, 35, 35, 35, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 35, 35, 35, 35, 35, 57, 57, 57, 35, 10, 10, 2, 2, 2, 3, 3, 1, 35, 70] 152 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 191 number of broken/clashed sets: 152 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220175 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 59, 76, 76, 35, 35, 35, 1, 1, 1, 1, 1, 4, 4, 4, 1, 7, 7, 35, 35, 35, 59, 59, 35, 1, 2] 152 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 36, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 270 number of broken/clashed sets: 152 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220175 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220175 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220175/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220175 Building REAL300000220176 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220176' /scratch/stefan/7769890/working/building/REAL300000220176 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220176 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220176/0 /scratch/stefan/7769890/working/building/REAL300000220176 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/177 `/scratch/stefan/7769890/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C([N+](=O)[O-])=C2)=N1) `REAL300000220176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220176 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [24, 24, 24, 24, 33, 33, 33, 24, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 24, 24, 24, 24, 33, 33, 24, 7, 7, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220176 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 24, 24, 17, 23, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 3, 1, 11, 11, 24, 24, 24] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 99 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220176 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220176 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220176/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220176 Building REAL300000220177 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220177' /scratch/stefan/7769890/working/building/REAL300000220177 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220177 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220177/0 /scratch/stefan/7769890/working/building/REAL300000220177 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/178 `/scratch/stefan/7769890/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)C=C2)N1) `REAL300000220177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220177 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 16, 22, 22, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 10, 10, 10, 10, 16, 16, 4, 4, 1, 1, 3, 3, 1, 3, 3, 1, 1, 10] 22 rigid atoms, others: [33, 34, 40, 41, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 42]) total number of confs: 84 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: REAL300000220177 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 6, 6, 10, 10, 6, 6, 14, 14, 8, 14, 14, 10, 10, 1, 2, 2, 2, 3, 3, 6, 6, 10, 10, 14, 14, 10, 14, 14, 10, 10, 1] 22 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 42] set([4, 5, 6, 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, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220177 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 22, 22, 22, 14, 14, 14, 6, 6, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 14, 14, 14, 22, 22, 6, 6, 3, 3, 1, 1, 1, 1, 1, 3, 3, 14] 22 rigid atoms, others: [35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220177 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220177 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220177/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220177 Building REAL300000220178 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220178' /scratch/stefan/7769890/working/building/REAL300000220178 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220178 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220178/0 /scratch/stefan/7769890/working/building/REAL300000220178 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/179 `/scratch/stefan/7769890/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1O) `REAL300000220178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220178 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 20, 20, 20, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 20, 20, 20, 35, 12, 20, 37, 37, 37, 20, 11, 11, 3, 3, 2, 2, 2, 1, 20, 35, 35, 35, 40] 150 rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41]) 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: REAL300000220178 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 37, 37, 37, 37, 37, 58, 72, 72, 37, 37, 37, 1, 1, 1, 3, 1, 1, 3, 3, 3, 1, 5, 5, 58, 58, 37, 37, 37, 37, 1, 3, 3, 3, 2] 154 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 23, 24, 28, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220178 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220178 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220178/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220178 Building REAL300000220179 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220179' /scratch/stefan/7769890/working/building/REAL300000220179 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220179 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220179/0 /scratch/stefan/7769890/working/building/REAL300000220179 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/180 `/scratch/stefan/7769890/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1O) `REAL300000220179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220179 none CCOC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [171, 131, 41, 41, 41, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 41, 41, 41, 41, 171, 171, 171, 171, 171, 41, 10, 10, 3, 3, 2, 2, 2, 1, 41, 41, 82] 402 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 529 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220179 none CCOC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [30, 7, 1, 1, 1, 1, 1, 5, 5, 41, 41, 41, 41, 41, 72, 119, 119, 41, 41, 41, 1, 1, 1, 1, 30, 30, 30, 30, 30, 1, 5, 5, 72, 72, 41, 41, 41, 41, 1, 1, 2] 402 rigid atoms, others: [2, 3, 4, 5, 6, 39, 20, 21, 22, 23, 38, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 515 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220179 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220179 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220179/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220179 Building REAL300000220180 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220180' /scratch/stefan/7769890/working/building/REAL300000220180 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220180 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220180/0 /scratch/stefan/7769890/working/building/REAL300000220180 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/181 `/scratch/stefan/7769890/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220180 none CSC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [41, 24, 18, 27, 27, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 27, 27, 41, 41, 41, 27, 27, 11, 11, 3, 3, 2, 2, 2, 1, 27, 27] 49 rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 137 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: REAL300000220180 none CSC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 37, 42, 42, 27, 27, 27, 1, 1, 6, 6, 6, 1, 1, 6, 6, 37, 37, 27, 27, 27, 27, 1, 1] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 20, 21, 25, 26, 36] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220180 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220180 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220180/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220180 Building REAL300000220181 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220181' /scratch/stefan/7769890/working/building/REAL300000220181 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220181 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220181/0 /scratch/stefan/7769890/working/building/REAL300000220181 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/182 `/scratch/stefan/7769890/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=CC=C2Cl)=N1) `REAL300000220181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220181 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=CC=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 21, 21, 21, 17, 17, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 21, 17, 4, 4, 1, 1, 1] 21 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 49 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: REAL300000220181 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=CC=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 17, 17, 17, 11, 17, 17, 17, 1, 2, 2, 2, 3, 3, 1, 11, 11, 17, 12, 17] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220181 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220181 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220181/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220181 Building REAL300000220182 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220182' /scratch/stefan/7769890/working/building/REAL300000220182 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220182 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220182/0 /scratch/stefan/7769890/working/building/REAL300000220182 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/183 `/scratch/stefan/7769890/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(OC)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220182 none COC1=CC(OC)=C(OC)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 53, 53, 53, 53, 53, 110, 53, 53, 122, 53, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 79, 79, 79, 53, 110, 110, 110, 122, 122, 122, 53, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [44, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 362 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220182 none COC1=CC(OC)=C(OC)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 1, 1, 9, 9, 53, 53, 53, 53, 53, 87, 120, 120, 53, 53, 53, 3, 3, 3, 1, 3, 3, 3, 4, 4, 4, 1, 9, 9, 53, 53, 53, 87, 87, 51] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 10, 11, 12, 36, 29] set([0, 6, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 424 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220182 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220182 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220182/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220182 Building REAL300000220183 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220183' /scratch/stefan/7769890/working/building/REAL300000220183 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220183 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220183/0 /scratch/stefan/7769890/working/building/REAL300000220183 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/184 `/scratch/stefan/7769890/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C)=C1) `REAL300000220183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220183 none CC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 10, 10, 10, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 3, 3, 2, 2, 2, 1, 10, 10, 10, 10] 15 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) 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: REAL300000220183 none CC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 15, 15, 15, 11, 11, 11, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 5, 15, 15, 11, 11, 11, 10, 2, 2, 2, 1] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 20, 21, 22, 26] set([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, 39, 40]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220183 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220183 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220183/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220183 Building REAL300000220184 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220184' /scratch/stefan/7769890/working/building/REAL300000220184 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220184 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220184/0 /scratch/stefan/7769890/working/building/REAL300000220184 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/185 `/scratch/stefan/7769890/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C(F)=C2)N1) `REAL300000220184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220184 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [19, 19, 19, 19, 27, 27, 27, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 27, 27, 6, 6, 1, 1, 1, 19] 27 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 79 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: REAL300000220184 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 9, 9, 19, 19, 19, 1] 27 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 59 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220184 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220184 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220184/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220184 Building REAL300000220185 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220185' /scratch/stefan/7769890/working/building/REAL300000220185 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220185 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220185/0 /scratch/stefan/7769890/working/building/REAL300000220185 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/186 `/scratch/stefan/7769890/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220185 none CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 28, 28, 111, 111, 111, 111, 111, 135, 135, 135, 111, 111, 111, 6, 6, 6, 1, 1, 1, 1, 1, 28, 28, 111, 111, 111, 135, 135, 111] 135 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 306 number of broken/clashed sets: 134 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220185 none CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 1, 11, 11, 61, 61, 61, 61, 61, 97, 135, 135, 61, 61, 61, 2, 2, 2, 6, 6, 1, 6, 6, 11, 11, 61, 61, 61, 97, 97, 61] 135 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 467 number of broken/clashed sets: 134 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220185 none CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 111, 111, 61, 111, 111, 61, 61, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 61, 61, 61, 111, 111, 61, 111, 111, 12, 12, 2, 2, 2, 3, 3, 1] 135 rigid atoms, others: [42, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 322 number of broken/clashed sets: 134 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220185 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220185 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220185/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220185 Building REAL300000220186 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220186' /scratch/stefan/7769890/working/building/REAL300000220186 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220186 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220186/0 /scratch/stefan/7769890/working/building/REAL300000220186 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/187 `/scratch/stefan/7769890/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3)=C2)=N1) `REAL300000220186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220186 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 73, 115, 115, 42, 42, 42, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 2, 6, 6, 1, 42, 42, 42, 42, 73, 73, 42, 5, 5, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 1] 201 rigid atoms, others: [36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 428 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220186 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 42, 42, 42, 42, 42, 75, 75, 148, 148, 83, 148, 148, 42, 1, 2, 2, 2, 3, 3, 1, 12, 12, 42, 42, 42, 75, 75, 148, 148, 148, 148, 148, 42] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 540 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220186 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 201, 201, 201, 148, 148, 148, 25, 25, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 148, 148, 148, 148, 201, 201, 148, 25, 25, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 531 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220186 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220186 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220186/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220186 Building REAL300000220187 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220187' /scratch/stefan/7769890/working/building/REAL300000220187 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220187 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220187/0 /scratch/stefan/7769890/working/building/REAL300000220187 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/188 `/scratch/stefan/7769890/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2Br)=N1) `REAL300000220187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220187 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [17, 17, 17, 17, 30, 30, 30, 17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 30, 30, 17, 7, 7, 1, 1, 1, 1] 30 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 109 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: REAL300000220187 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 17, 17, 9, 17, 17, 17, 1, 2, 2, 2, 3, 3, 1, 9, 9, 17, 17, 17, 17] 30 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 98 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220187 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220187 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220187/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220187 Building REAL300000220188 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220188' /scratch/stefan/7769890/working/building/REAL300000220188 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220188 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220188/0 /scratch/stefan/7769890/working/building/REAL300000220188 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/189 `/scratch/stefan/7769890/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1O) `REAL300000220188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220188 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [39, 25, 25, 25, 25, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 25, 25, 25, 39, 39, 39, 25, 25, 10, 10, 3, 3, 1, 1, 1, 1, 25, 50] 124 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 142 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: REAL300000220188 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 7, 7, 25, 25, 25, 25, 25, 41, 62, 62, 25, 25, 25, 1, 1, 1, 4, 4, 4, 1, 1, 7, 7, 41, 41, 25, 25, 25, 25, 1, 2] 124 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 229 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220188 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220188 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220188/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220188 Building REAL300000220189 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220189' /scratch/stefan/7769890/working/building/REAL300000220189 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220189 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220189/0 /scratch/stefan/7769890/working/building/REAL300000220189 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/190 `/scratch/stefan/7769890/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220189 none COC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [39, 39, 19, 39, 12, 29, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 29, 39, 39, 39, 29, 29, 11, 11, 3, 3, 2, 2, 2, 1, 29, 29] 51 rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 182 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: REAL300000220189 none COC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [6, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 46, 50, 50, 29, 29, 29, 1, 1, 7, 7, 7, 1, 1, 6, 6, 46, 46, 29, 29, 29, 29, 1, 1] 51 rigid atoms, others: [2, 4, 5, 6, 7, 8, 38, 22, 23, 27, 28, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 177 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220189 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220189 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220189/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220189 Building REAL300000220190 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220190' /scratch/stefan/7769890/working/building/REAL300000220190 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220190 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220190/0 /scratch/stefan/7769890/working/building/REAL300000220190 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/191 `/scratch/stefan/7769890/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1) `REAL300000220190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220190 none COC(=O)C1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [13, 13, 1, 13, 1, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 38, 38, 38, 38, 38, 62, 70, 70, 38, 39, 38, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1, 8, 8, 39, 39, 39, 62, 62, 38, 13, 13] 201 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 34, 26] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 286 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220190 none COC(=O)C1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 13, 13, 13, 13, 38, 38, 147, 147, 147, 147, 147, 201, 201, 201, 147, 147, 147, 13, 1, 1, 6, 6, 6, 1, 1, 13, 13, 38, 38, 147, 147, 147, 201, 201, 147, 1, 1] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 44, 45, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 560 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220190 none COC(=O)C1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [151, 151, 38, 151, 38, 147, 147, 38, 38, 38, 38, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 38, 147, 147, 151, 151, 151, 147, 147, 38, 39, 11, 11, 2, 2, 2, 3, 3, 1, 147, 147] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 682 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220190 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220190 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220190/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220190 Building REAL300000220191 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220191' /scratch/stefan/7769890/working/building/REAL300000220191 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220191 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220191/0 /scratch/stefan/7769890/working/building/REAL300000220191 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/192 `/scratch/stefan/7769890/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC4=CC=CC=C43)C=C2)N1) `REAL300000220191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220191 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC4=CC=CC=C43)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 35, 48, 48, 22, 22, 22, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 22, 22, 22, 22, 35, 35, 3, 3, 1, 1, 11, 11, 11, 11, 11, 1, 1, 22] 78 rigid atoms, others: [36, 37, 44, 43, 12, 13, 14, 15, 16, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 45]) total number of confs: 169 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220191 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC4=CC=CC=C43)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 22, 22, 12, 12, 63, 63, 63, 63, 63, 63, 63, 63, 22, 22, 1, 2, 2, 2, 3, 3, 12, 12, 22, 22, 63, 63, 63, 63, 63, 22, 22, 1] 78 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 45, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220191 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=NC4=CC=CC=C43)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 78, 78, 78, 62, 63, 62, 19, 19, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 63, 63, 63, 63, 78, 78, 19, 19, 11, 11, 1, 1, 1, 1, 1, 11, 11, 63] 78 rigid atoms, others: [38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45]) total number of confs: 214 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220191 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220191 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220191/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220191 Building REAL300000220192 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220192' /scratch/stefan/7769890/working/building/REAL300000220192 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220192 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220192/0 /scratch/stefan/7769890/working/building/REAL300000220192 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/193 `/scratch/stefan/7769890/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)NC3=CC=CC=C32)N1) `REAL300000220192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220192 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)NC3=CC=CC=C32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 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: [43, 43, 43, 43, 51, 51, 51, 42, 43, 43, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 51, 51, 11, 11, 1, 1, 1, 1, 1, 43] 51 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 115 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: REAL300000220192 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)NC3=CC=CC=C32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 2, 2, 2, 3, 3, 11, 11, 43, 43, 43, 43, 43, 1] 51 rigid atoms, others: [0, 1, 2, 3, 36, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220192 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220192 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220192/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220192 Building REAL300000220193 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220193' /scratch/stefan/7769890/working/building/REAL300000220193 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220193 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220193/0 /scratch/stefan/7769890/working/building/REAL300000220193 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/194 `/scratch/stefan/7769890/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCCC3)N=C2)=N1) `REAL300000220193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220193 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 21, 34, 34, 17, 17, 17, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 17, 17, 17, 17, 21, 21, 17, 3, 3, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1] 61 rigid atoms, others: [33, 42, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220193 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 17, 17, 10, 10, 60, 60, 60, 60, 17, 17, 1, 2, 2, 2, 3, 3, 1, 10, 10, 17, 60, 60, 60, 60, 60, 60, 60, 60, 17] 61 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220193 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 61, 61, 61, 60, 60, 60, 15, 15, 1, 1, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 60, 60, 60, 60, 61, 61, 60, 15, 15, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9] 61 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42]) total number of confs: 115 number of broken/clashed sets: 60 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220193 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220193 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220193/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220193 Building REAL300000220194 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220194' /scratch/stefan/7769890/working/building/REAL300000220194 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220194 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220194/0 /scratch/stefan/7769890/working/building/REAL300000220194 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/195 `/scratch/stefan/7769890/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCCOC3=C2)=N1) `REAL300000220194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220194 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 33, 33, 33, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 33, 33, 21, 6, 6, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 106 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220194 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 7, 7, 21, 21, 21, 21, 21, 21] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 58 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220194 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220194 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220194/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220194 Building REAL300000220195 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220195' /scratch/stefan/7769890/working/building/REAL300000220195 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220195 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220195/0 /scratch/stefan/7769890/working/building/REAL300000220195 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/196 `/scratch/stefan/7769890/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)C3=CC=CC=C3S2)N1) `REAL300000220195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220195 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)C3=CC=CC=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 25, 39, 39, 39, 25, 25, 25, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 39, 39, 9, 9, 1, 1, 1, 1, 25] 39 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 127 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: REAL300000220195 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)C3=CC=CC=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 11, 11, 25, 25, 25, 25, 1] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220195 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220195 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220195/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220195 Building REAL300000220196 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220196' /scratch/stefan/7769890/working/building/REAL300000220196 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220196 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220196/0 /scratch/stefan/7769890/working/building/REAL300000220196 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/197 `/scratch/stefan/7769890/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCCCOC3=C2)=N1) `REAL300000220196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220196 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCCCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 12, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 33, 33, 33, 23, 23, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 33, 33, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 32, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 95 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220196 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C3OCCCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 12, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 3, 1, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220196 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220196 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220196/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220196 Building REAL300000220197 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220197' /scratch/stefan/7769890/working/building/REAL300000220197 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220197 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220197/0 /scratch/stefan/7769890/working/building/REAL300000220197 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/198 `/scratch/stefan/7769890/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(F)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220197 none CC1=NN(C2=CC=C(F)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 24, 24, 74, 74, 74, 74, 74, 96, 96, 96, 74, 74, 74, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 24, 24, 74, 74, 74, 96, 96, 74] 96 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 249 number of broken/clashed sets: 95 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220197 none CC1=NN(C2=CC=C(F)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 1, 1, 6, 6, 1, 1, 1, 1, 9, 9, 49, 49, 49, 49, 49, 70, 92, 92, 49, 49, 49, 2, 2, 2, 6, 6, 6, 6, 2, 2, 2, 9, 9, 49, 49, 49, 70, 70, 49] 96 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 306 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220197 none CC1=NN(C2=CC=C(F)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 74, 74, 49, 49, 74, 74, 49, 49, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 49, 49, 49, 74, 74, 74, 74, 49, 49, 49, 11, 11, 2, 2, 2, 3, 3, 1] 96 rigid atoms, others: [45, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 220 number of broken/clashed sets: 95 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220197 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220197 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220197/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220197 Building REAL300000220198 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220198' /scratch/stefan/7769890/working/building/REAL300000220198 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220198 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220198/0 /scratch/stefan/7769890/working/building/REAL300000220198 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/199 `/scratch/stefan/7769890/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=C2)N1) `REAL300000220198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220198 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 28, 28, 28, 39, 39, 39, 28, 28, 28, 6, 6, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 28, 28, 28, 28, 39, 39, 6, 6, 1, 4, 4, 1, 4, 4, 1, 28] 39 rigid atoms, others: [32, 38, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 39]) total number of confs: 116 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: REAL300000220198 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 28, 28, 28, 35, 35, 28, 35, 35, 28, 28, 1, 2, 2, 2, 3, 3, 9, 9, 28, 35, 35, 28, 35, 35, 28, 1] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220198 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [35, 35, 35, 35, 39, 39, 39, 35, 35, 35, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 39, 39, 12, 12, 4, 1, 1, 1, 1, 1, 4, 35] 39 rigid atoms, others: [33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 83 number of broken/clashed sets: 38 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220198 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220198 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220198/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220198 Building REAL300000220199 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220199' /scratch/stefan/7769890/working/building/REAL300000220199 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220199 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220199/0 /scratch/stefan/7769890/working/building/REAL300000220199 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/200 `/scratch/stefan/7769890/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1F) `REAL300000220199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220199 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [37, 24, 23, 24, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 24, 24, 24, 37, 37, 37, 24, 24, 10, 10, 3, 3, 2, 2, 2, 1, 24] 62 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 100 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: REAL300000220199 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 40, 62, 62, 24, 24, 24, 1, 1, 1, 3, 3, 3, 1, 1, 6, 6, 40, 40, 24, 24, 24, 24, 1] 62 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 223 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220199 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220199 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220199/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220199 Building REAL300000220200 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220200' /scratch/stefan/7769890/working/building/REAL300000220200 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220200 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220200/0 /scratch/stefan/7769890/working/building/REAL300000220200 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/201 `/scratch/stefan/7769890/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220200 none COC1=CC=C(C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [77, 63, 63, 63, 41, 63, 63, 63, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 77, 77, 77, 63, 63, 63, 63, 63, 63, 11, 11, 3, 3, 2, 2, 2, 1] 98 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 231 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: REAL300000220200 none COC1=CC=C(C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 63, 63, 63, 63, 63, 92, 98, 98, 63, 63, 63, 4, 4, 4, 1, 1, 2, 2, 2, 1, 11, 11, 92, 92, 63, 63, 63, 63] 98 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 298 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220200 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220200 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220200/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220200 Building REAL300000220201 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220201' /scratch/stefan/7769890/working/building/REAL300000220201 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220201 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220201/0 /scratch/stefan/7769890/working/building/REAL300000220201 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/202 `/scratch/stefan/7769890/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3)N=C2)=N1) `REAL300000220201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220201 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 68, 87, 87, 38, 38, 38, 7, 7, 1, 1, 1, 1, 1, 7, 11, 11, 9, 11, 11, 1, 1, 38, 38, 38, 38, 68, 68, 38, 7, 7, 1, 7, 7, 11, 11, 11, 11, 11, 1] 201 rigid atoms, others: [34, 42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 347 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220201 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 38, 38, 38, 125, 148, 148, 137, 148, 148, 38, 38, 1, 2, 2, 2, 3, 3, 1, 10, 10, 38, 125, 125, 148, 148, 147, 148, 148, 38] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 540 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220201 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 201, 201, 201, 148, 148, 148, 41, 41, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 148, 148, 148, 148, 201, 201, 148, 41, 41, 11, 3, 3, 1, 1, 1, 1, 1, 11] 201 rigid atoms, others: [37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 560 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220201 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220201 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220201/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220201 Building REAL300000220202 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220202' /scratch/stefan/7769890/working/building/REAL300000220202 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220202 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220202/0 /scratch/stefan/7769890/working/building/REAL300000220202 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/203 `/scratch/stefan/7769890/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)S2)=N1) `REAL300000220202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220202 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [48, 48, 48, 48, 61, 63, 63, 48, 48, 48, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 2, 2, 7, 7, 1, 48, 48, 48, 48, 61, 61, 48, 12, 12, 1, 1, 7, 7, 7, 7] 95 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 170 number of broken/clashed sets: 94 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220202 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 48, 48, 48, 48, 79, 79, 73, 74, 79, 79, 48, 1, 2, 2, 2, 3, 3, 1, 11, 11, 48, 48, 79, 79, 79, 79] 95 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 165 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220202 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [79, 79, 79, 79, 95, 95, 95, 79, 79, 79, 37, 37, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 79, 79, 79, 79, 95, 95, 79, 37, 37, 7, 7, 1, 1, 1, 1] 95 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 239 number of broken/clashed sets: 94 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220202 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220202 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220202/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220202 Building REAL300000220203 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220203' /scratch/stefan/7769890/working/building/REAL300000220203 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220203 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220203/0 /scratch/stefan/7769890/working/building/REAL300000220203 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/204 `/scratch/stefan/7769890/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC([N+](=O)[O-])=CC3=C2OCOC3)=N1) `REAL300000220203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220203 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC([N+](=O)[O-])=CC3=C2OCOC3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 5, 12, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 53, 53, 53, 38, 38, 38, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 53, 53, 38, 11, 11, 1, 1, 1, 1, 1, 1] 53 rigid atoms, others: [35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 33, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 148 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: REAL300000220203 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC([N+](=O)[O-])=CC3=C2OCOC3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 5, 12, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 2, 2, 2, 3, 3, 1, 9, 9, 38, 38, 38, 38, 38, 38] 53 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 79 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220203 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220203 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220203/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220203 Building REAL300000220204 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220204' /scratch/stefan/7769890/working/building/REAL300000220204 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220204 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220204/0 /scratch/stefan/7769890/working/building/REAL300000220204 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/205 `/scratch/stefan/7769890/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C2O1) `REAL300000220204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220204 none CCC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [106, 62, 62, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 62, 62, 62, 62, 62, 62, 62, 106, 106, 106, 106, 106, 12, 12, 3, 3, 2, 2, 2, 1, 62, 62, 62, 62] 130 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 347 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: REAL300000220204 none CCC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 11, 11, 62, 61, 62, 62, 62, 90, 99, 99, 62, 62, 62, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 11, 11, 90, 90, 62, 62, 62, 62, 1, 1, 1, 1] 130 rigid atoms, others: [1, 2, 3, 4, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 313 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220204 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220204 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220204/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220204 Building REAL300000220205 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220205' /scratch/stefan/7769890/working/building/REAL300000220205 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220205 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220205/0 /scratch/stefan/7769890/working/building/REAL300000220205 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/206 `/scratch/stefan/7769890/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3F)C=C2)=N1) `REAL300000220205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220205 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 45, 66, 66, 28, 28, 28, 4, 4, 1, 1, 1, 1, 1, 1, 2, 6, 24, 24, 12, 24, 24, 24, 1, 1, 28, 28, 28, 28, 45, 45, 28, 4, 4, 1, 1, 6, 6, 24, 24, 24, 24, 1, 1] 201 rigid atoms, others: [45, 37, 38, 12, 13, 14, 15, 16, 17, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 302 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220205 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 13, 13, 28, 28, 16, 18, 45, 73, 151, 151, 119, 151, 151, 151, 28, 28, 1, 2, 2, 2, 3, 3, 1, 13, 13, 28, 28, 73, 73, 151, 151, 151, 151, 28, 28] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 552 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220205 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC=C3F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 151, 201, 201, 201, 151, 151, 151, 49, 49, 24, 18, 25, 25, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 151, 151, 151, 151, 201, 201, 151, 49, 49, 25, 25, 8, 8, 1, 1, 1, 1, 24, 24] 201 rigid atoms, others: [41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46]) total number of confs: 617 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220205 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220205 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220205/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220205 Building REAL300000220206 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220206' /scratch/stefan/7769890/working/building/REAL300000220206 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220206 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220206/0 /scratch/stefan/7769890/working/building/REAL300000220206 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/207 `/scratch/stefan/7769890/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(C)=O)C1=NC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1) `REAL300000220206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220206 none CCN(C(C)=O)C1=NC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.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, 5, 11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 99, 68, 99, 107, 107, 68, 68, 13, 13, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 68, 68, 167, 167, 167, 167, 167, 107, 107, 107, 13, 13, 2, 2, 2, 3, 3, 1, 68] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 661 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220206 none CCN(C(C)=O)C1=NC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.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, 5, 11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 1, 6, 10, 10, 1, 1, 1, 1, 12, 12, 68, 68, 68, 68, 68, 98, 106, 106, 68, 68, 68, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 68, 68, 68, 98, 98, 64, 1] 201 rigid atoms, others: [2, 6, 7, 8, 9, 41, 23, 24] set([0, 1, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 358 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220206 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220206 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220206/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220206 Building REAL300000220207 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220207' /scratch/stefan/7769890/working/building/REAL300000220207 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220207 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220207/0 /scratch/stefan/7769890/working/building/REAL300000220207 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/208 `/scratch/stefan/7769890/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(F)C=C3)=N2)=N1) `REAL300000220207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220207 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(F)C=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 45, 46, 46, 65, 65, 65, 46, 46, 46, 12, 12, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 45, 46, 46, 46, 65, 65, 44, 12, 12, 1, 3, 3, 3, 3] 65 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 196 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220207 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(F)C=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 46, 46, 46, 46, 53, 53, 46, 46, 53, 53, 46, 1, 2, 2, 2, 3, 3, 1, 11, 11, 46, 53, 53, 53, 53] 65 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220207 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C(F)C=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [53, 53, 53, 53, 65, 65, 65, 53, 53, 53, 22, 22, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 53, 53, 53, 53, 65, 65, 53, 22, 22, 3, 1, 1, 1, 1] 65 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 165 number of broken/clashed sets: 64 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220207 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220207 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220207/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220207 Building REAL300000220208 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220208' /scratch/stefan/7769890/working/building/REAL300000220208 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220208 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220208/0 /scratch/stefan/7769890/working/building/REAL300000220208 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/209 `/scratch/stefan/7769890/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC(F)=C3)C=C2)=N1) `REAL300000220208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220208 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC(F)=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 39, 59, 59, 24, 24, 24, 4, 4, 1, 1, 1, 1, 1, 1, 2, 6, 32, 32, 32, 32, 32, 32, 1, 1, 24, 24, 24, 24, 39, 39, 24, 4, 4, 1, 1, 6, 6, 32, 32, 32, 32, 1, 1] 201 rigid atoms, others: [45, 37, 38, 12, 13, 14, 15, 16, 17, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 252 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220208 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC(F)=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 24, 24, 12, 19, 40, 68, 169, 169, 169, 169, 169, 169, 24, 24, 1, 2, 2, 2, 3, 3, 1, 12, 12, 24, 24, 68, 68, 169, 169, 169, 169, 24, 24] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 435 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220208 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=CC(F)=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 169, 201, 201, 201, 169, 169, 169, 63, 63, 32, 18, 32, 32, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 169, 169, 169, 169, 201, 201, 169, 63, 63, 32, 32, 8, 8, 1, 1, 1, 1, 32, 32] 201 rigid atoms, others: [41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46]) total number of confs: 598 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220208 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220208 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220208/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220208 Building REAL300000220209 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220209' /scratch/stefan/7769890/working/building/REAL300000220209 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220209 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220209/0 /scratch/stefan/7769890/working/building/REAL300000220209 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/210 `/scratch/stefan/7769890/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(NC(=O)C(F)(F)F)=C2)=N1) `REAL300000220209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220209 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(NC(=O)C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 79, 100, 100, 47, 47, 47, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 47, 47, 47, 47, 79, 79, 47, 6, 6, 1, 1, 1, 9, 1] 201 rigid atoms, others: [35, 36, 37, 39, 12, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 353 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220209 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(NC(=O)C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 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 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 47, 47, 47, 47, 47, 146, 146, 146, 146, 146, 146, 47, 1, 2, 2, 2, 3, 3, 1, 12, 12, 47, 47, 47, 146, 47] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 355 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220209 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220209 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220209/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220209 Building REAL300000220210 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220210' /scratch/stefan/7769890/working/building/REAL300000220210 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220210 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220210/0 /scratch/stefan/7769890/working/building/REAL300000220210 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/211 `/scratch/stefan/7769890/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])O2)=N1) `REAL300000220210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220210 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [75, 74, 75, 75, 118, 150, 150, 75, 75, 75, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 7, 7, 1, 74, 75, 75, 75, 118, 118, 75, 13, 13, 1, 1, 7, 7, 2, 7] 185 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 505 number of broken/clashed sets: 184 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220210 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 75, 75, 75, 75, 143, 143, 103, 143, 143, 143, 143, 143, 75, 1, 2, 2, 2, 3, 3, 1, 11, 11, 75, 75, 143, 143, 105, 143] 185 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 348 number of broken/clashed sets: 184 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220210 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [143, 143, 143, 143, 185, 185, 185, 143, 143, 143, 41, 41, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 143, 143, 143, 143, 185, 185, 143, 41, 41, 7, 7, 1, 1, 1, 1] 185 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 475 number of broken/clashed sets: 184 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220210 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220210 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220210/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220210 Building REAL300000220211 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220211' /scratch/stefan/7769890/working/building/REAL300000220211 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220211 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220211/0 /scratch/stefan/7769890/working/building/REAL300000220211 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/212 `/scratch/stefan/7769890/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)C=C1) `REAL300000220211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220211 none COC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 2, 4, 4, 1, 1, 1, 1, 1, 12, 12, 55, 55, 56, 56, 56, 90, 116, 116, 56, 56, 56, 1, 1, 4, 4, 5, 5, 5, 4, 4, 12, 12, 56, 56, 56, 90, 90, 54, 1, 4, 4] 116 rigid atoms, others: [5, 6, 7, 8, 9, 40, 23, 24] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 410 number of broken/clashed sets: 115 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220211 none COC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 34, 34, 92, 92, 92, 92, 92, 116, 116, 116, 92, 92, 92, 4, 4, 1, 1, 2, 2, 2, 1, 1, 34, 34, 92, 92, 92, 116, 116, 90, 4, 1, 1] 116 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 304 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220211 none COC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [92, 86, 85, 92, 92, 56, 56, 56, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 56, 56, 92, 92, 92, 92, 92, 92, 92, 12, 12, 2, 2, 2, 3, 3, 1, 56, 92, 92] 116 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 208 number of broken/clashed sets: 115 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220211 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220211 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220211/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220211 Building REAL300000220212 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220212' /scratch/stefan/7769890/working/building/REAL300000220212 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220212 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220212/0 /scratch/stefan/7769890/working/building/REAL300000220212 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/213 `/scratch/stefan/7769890/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(Cl)=C1) `REAL300000220212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220212 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [37, 25, 19, 31, 31, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 31, 31, 31, 37, 37, 37, 31, 31, 12, 12, 3, 3, 2, 2, 2, 1, 31] 61 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 134 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: REAL300000220212 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [2, 1, 1, 1, 1, 1, 1, 9, 9, 31, 31, 31, 31, 31, 49, 61, 61, 31, 31, 31, 1, 1, 1, 3, 3, 3, 1, 1, 9, 9, 49, 49, 31, 31, 31, 31, 1] 61 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 211 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220212 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220212 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220212/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220212 Building REAL300000220213 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220213' /scratch/stefan/7769890/working/building/REAL300000220213 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220213 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220213/0 /scratch/stefan/7769890/working/building/REAL300000220213 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/214 `/scratch/stefan/7769890/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1O) `REAL300000220213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220213 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [44, 30, 30, 30, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 30, 30, 30, 30, 44, 44, 44, 30, 12, 12, 3, 3, 2, 2, 2, 1, 30, 30, 60] 116 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 164 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: REAL300000220213 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 1, 1, 1, 1, 6, 6, 30, 30, 30, 30, 30, 45, 58, 58, 30, 30, 30, 1, 1, 1, 1, 3, 3, 3, 1, 6, 6, 45, 45, 30, 30, 30, 30, 1, 1, 2] 116 rigid atoms, others: [1, 2, 3, 4, 5, 35, 19, 20, 21, 22, 36, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 37]) total number of confs: 190 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220213 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220213 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220213/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220213 Building REAL300000220214 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220214' /scratch/stefan/7769890/working/building/REAL300000220214 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220214 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220214/0 /scratch/stefan/7769890/working/building/REAL300000220214 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/215 `/scratch/stefan/7769890/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(Cl)=C2)N1) `REAL300000220214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220214 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [18, 18, 18, 18, 27, 27, 27, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 27, 27, 6, 6, 1, 1, 1, 1, 18] 27 rigid atoms, others: [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, 32, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 83 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: REAL300000220214 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 8, 8, 18, 18, 16, 18, 18, 18, 1, 2, 2, 2, 3, 3, 8, 8, 18, 18, 17, 18, 1] 27 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 20] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 63 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220214 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220214 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220214/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220214 Building REAL300000220215 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220215' /scratch/stefan/7769890/working/building/REAL300000220215 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220215 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220215/0 /scratch/stefan/7769890/working/building/REAL300000220215 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/216 `/scratch/stefan/7769890/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C=C2)=N1) `REAL300000220215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220215 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 31, 49, 49, 17, 17, 17, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 17, 17, 17, 17, 31, 31, 17, 3, 3, 1, 1, 10, 10, 10, 11, 10, 10, 10, 10, 10, 10, 1, 1] 63 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 46, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 189 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: REAL300000220215 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 17, 17, 11, 11, 52, 52, 52, 52, 52, 17, 17, 1, 2, 2, 2, 3, 3, 1, 11, 11, 17, 17, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 17, 17] 63 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220215 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCCCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 52, 52, 52, 63, 63, 63, 52, 52, 52, 17, 17, 1, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 52, 52, 52, 52, 63, 63, 52, 17, 17, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 63 rigid atoms, others: [45, 36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47]) total number of confs: 171 number of broken/clashed sets: 63 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220215 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220215 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220215/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220215 Building REAL300000220216 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220216' /scratch/stefan/7769890/working/building/REAL300000220216 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220216 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220216/0 /scratch/stefan/7769890/working/building/REAL300000220216 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/217 `/scratch/stefan/7769890/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(F)C=C3)O2)=N1) `REAL300000220216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220216 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(F)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [61, 60, 61, 61, 90, 120, 120, 61, 61, 61, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 2, 4, 7, 7, 1, 60, 61, 61, 61, 90, 90, 61, 13, 13, 1, 1, 7, 7, 7, 7] 120 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 400 number of broken/clashed sets: 119 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220216 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(F)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 61, 61, 61, 61, 95, 95, 85, 95, 95, 95, 61, 1, 2, 2, 2, 3, 3, 1, 12, 12, 61, 61, 95, 95, 95, 95] 120 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 225 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220216 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(F)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 120, 120, 120, 95, 95, 95, 42, 42, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 95, 95, 95, 95, 120, 120, 95, 42, 42, 7, 7, 1, 1, 1, 1] 120 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 313 number of broken/clashed sets: 119 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220216 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220216 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220216/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220216 Building REAL300000220217 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220217' /scratch/stefan/7769890/working/building/REAL300000220217 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220217 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220217/0 /scratch/stefan/7769890/working/building/REAL300000220217 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/218 `/scratch/stefan/7769890/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3Cl)N=C2)=N1) `REAL300000220217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220217 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3Cl)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 42, 48, 48, 27, 27, 27, 6, 6, 1, 1, 1, 1, 1, 7, 11, 11, 9, 11, 11, 11, 1, 1, 27, 27, 27, 27, 42, 42, 27, 6, 6, 1, 7, 7, 11, 11, 11, 11, 1] 201 rigid atoms, others: [35, 42, 12, 13, 14, 15, 16, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220217 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3Cl)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 78, 138, 138, 111, 138, 138, 138, 27, 27, 1, 2, 2, 2, 3, 3, 1, 9, 9, 27, 78, 78, 138, 138, 138, 138, 27] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 515 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220217 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CC=C3Cl)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 8, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 138, 138, 138, 201, 201, 201, 138, 138, 138, 38, 38, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 138, 138, 138, 138, 201, 201, 138, 38, 38, 11, 5, 5, 1, 1, 1, 1, 11] 201 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 611 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220217 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220217 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220217/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220217 Building REAL300000220218 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220218' /scratch/stefan/7769890/working/building/REAL300000220218 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220218 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220218/0 /scratch/stefan/7769890/working/building/REAL300000220218 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/219 `/scratch/stefan/7769890/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C(=NC(C)=C2C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1) `REAL300000220218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220218 none CC1=CN2C(=NC(C)=C2C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [35, 31, 35, 35, 35, 35, 35, 35, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 12, 12, 2, 2, 2, 3, 3, 1] 49 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 95 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: REAL300000220218 none CC1=CN2C(=NC(C)=C2C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 1, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 49, 49, 49, 35, 35, 35, 1, 2, 2, 2, 1, 2, 2, 2, 7, 7, 35, 35, 35, 49, 49, 35] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220218 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220218 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220218/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220218 Building REAL300000220219 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220219' /scratch/stefan/7769890/working/building/REAL300000220219 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220219 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220219/0 /scratch/stefan/7769890/working/building/REAL300000220219 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/220 `/scratch/stefan/7769890/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OC(F)(F)F)=N1) `REAL300000220219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220219 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 61, 79, 79, 43, 43, 43, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 43, 43, 43, 43, 61, 61, 43, 7, 7, 1, 1, 1, 1] 81 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 278 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220219 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 43, 43, 19, 43, 43, 43, 67, 74, 74, 74, 1, 2, 2, 2, 3, 3, 1, 12, 12, 43, 43, 43, 43] 81 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 265 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220219 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220219 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220219/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220219 Building REAL300000220220 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220220' /scratch/stefan/7769890/working/building/REAL300000220220 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220220 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220220/0 /scratch/stefan/7769890/working/building/REAL300000220220 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/221 `/scratch/stefan/7769890/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SC(F)(F)F)C=C2)=N1) `REAL300000220220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220220 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SC(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 23, 23, 37, 53, 53, 23, 23, 23, 4, 4, 1, 1, 1, 1, 1, 1, 12, 22, 22, 22, 1, 1, 23, 23, 23, 23, 37, 37, 23, 4, 4, 1, 1, 1, 1] 101 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 242 number of broken/clashed sets: 101 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220220 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SC(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 23, 23, 23, 23, 66, 67, 67, 67, 23, 23, 1, 2, 2, 2, 3, 3, 1, 12, 12, 23, 23, 23, 23] 101 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 137 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220220 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220220 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220220/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220220 Building REAL300000220221 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220221' /scratch/stefan/7769890/working/building/REAL300000220221 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220221 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220221/0 /scratch/stefan/7769890/working/building/REAL300000220221 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/222 `/scratch/stefan/7769890/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=NC=C3)C=C2)=N1) `REAL300000220221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220221 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=NC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 39, 59, 59, 23, 23, 23, 4, 4, 1, 1, 1, 1, 1, 1, 4, 12, 28, 28, 12, 28, 28, 1, 1, 23, 23, 23, 23, 39, 39, 23, 4, 4, 1, 1, 12, 12, 28, 28, 28, 28, 1, 1] 201 rigid atoms, others: [45, 36, 37, 44, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 291 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220221 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=NC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 23, 23, 12, 12, 39, 100, 152, 152, 100, 152, 151, 23, 23, 1, 2, 2, 2, 3, 3, 1, 12, 12, 23, 23, 101, 101, 152, 152, 152, 152, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 621 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220221 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=NC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 152, 152, 152, 201, 201, 201, 152, 152, 152, 50, 50, 25, 25, 28, 28, 15, 5, 1, 1, 1, 1, 1, 1, 1, 28, 28, 152, 152, 152, 152, 201, 201, 152, 50, 50, 28, 28, 5, 5, 1, 1, 1, 1, 28, 28] 201 rigid atoms, others: [40, 41, 42, 43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45]) total number of confs: 582 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220221 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220221 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220221/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220221 Building REAL300000220222 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220222' /scratch/stefan/7769890/working/building/REAL300000220222 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220222 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220222/0 /scratch/stefan/7769890/working/building/REAL300000220222 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/223 `/scratch/stefan/7769890/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])S2)=N1) `REAL300000220222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220222 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 92, 106, 106, 67, 67, 67, 13, 13, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 67, 67, 67, 67, 92, 92, 67, 13, 13, 1, 1, 5, 5, 5, 5] 120 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 304 number of broken/clashed sets: 119 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220222 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 67, 99, 99, 99, 99, 99, 99, 99, 99, 67, 1, 2, 2, 2, 3, 3, 1, 12, 12, 67, 67, 99, 99, 99, 99] 120 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 172 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220222 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3[N+](=O)[O-])S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 120, 120, 120, 99, 99, 99, 37, 37, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 99, 99, 99, 99, 120, 120, 99, 37, 37, 5, 5, 1, 1, 1, 1] 120 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 293 number of broken/clashed sets: 119 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220222 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220222 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220222/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220222 Building REAL300000220223 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220223' /scratch/stefan/7769890/working/building/REAL300000220223 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220223 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220223/0 /scratch/stefan/7769890/working/building/REAL300000220223 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/224 `/scratch/stefan/7769890/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(O)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220223 none COC1=CC(O)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [60, 49, 49, 49, 19, 49, 49, 49, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 60, 60, 60, 49, 98, 49, 49, 12, 12, 3, 3, 2, 2, 2, 1] 150 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 316 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: REAL300000220223 none COC1=CC(O)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 49, 49, 49, 49, 49, 67, 75, 75, 49, 49, 49, 3, 3, 3, 1, 2, 1, 1, 11, 11, 67, 67, 49, 49, 49, 49] 150 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 28, 29] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 213 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220223 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220223 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220223/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220223 Building REAL300000220224 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220224' /scratch/stefan/7769890/working/building/REAL300000220224 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220224 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220224/0 /scratch/stefan/7769890/working/building/REAL300000220224 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/225 `/scratch/stefan/7769890/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC2=C1OCCO2) `REAL300000220224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220224 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [39, 28, 28, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 39, 39, 39, 28, 11, 11, 2, 2, 2, 3, 3, 1, 28, 28, 28, 28, 28] 65 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 94 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: REAL300000220224 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 49, 65, 65, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 6, 6, 28, 28, 28, 49, 49, 28, 1, 1, 1, 1, 1] 65 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 234 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220224 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220224 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220224/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220224 Building REAL300000220225 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220225' /scratch/stefan/7769890/working/building/REAL300000220225 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220225 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220225/0 /scratch/stefan/7769890/working/building/REAL300000220225 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/226 `/scratch/stefan/7769890/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(F)C=CC=C2F)N1) `REAL300000220225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220225 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(F)C=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [14, 14, 14, 14, 22, 22, 22, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 22, 5, 5, 1, 1, 1, 14] 22 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 71 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: REAL300000220225 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(F)C=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 3, 3, 11, 11, 16, 16, 16, 1] 22 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220225 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220225 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220225/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220225 Building REAL300000220226 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220226' /scratch/stefan/7769890/working/building/REAL300000220226 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220226 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220226/0 /scratch/stefan/7769890/working/building/REAL300000220226 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/227 `/scratch/stefan/7769890/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=CO1) `REAL300000220226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220226 none COC(=O)C1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 164, 79, 165, 79, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 79, 79, 79, 165, 165, 165, 12, 12, 2, 2, 2, 3, 3, 1, 79, 79] 201 rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 402 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220226 none COC(=O)C1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 11, 11, 79, 79, 79, 79, 79, 130, 167, 167, 79, 79, 79, 1, 1, 1, 13, 13, 13, 11, 11, 79, 79, 79, 130, 130, 79, 1, 1] 201 rigid atoms, others: [2, 35, 4, 5, 6, 34, 20, 21, 22] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 584 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220226 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220226 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220226/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220226 Building REAL300000220227 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220227' /scratch/stefan/7769890/working/building/REAL300000220227 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220227 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220227/0 /scratch/stefan/7769890/working/building/REAL300000220227 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/228 `/scratch/stefan/7769890/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(C)N1C1CCCCC1) `REAL300000220227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220227 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(C)N1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 43, 43, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 43, 43, 43, 43, 61, 61, 61, 61, 61, 43, 43, 43, 43, 12, 12, 2, 2, 2, 3, 3, 1, 43, 43, 43, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61] 89 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220227 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(C)N1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 43, 43, 43, 43, 43, 61, 71, 71, 43, 43, 43, 1, 1, 1, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 12, 12, 43, 43, 43, 61, 61, 43, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 89 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 231 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220227 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(C)N1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 21, 21, 61, 61, 61, 61, 61, 89, 89, 89, 61, 61, 61, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 21, 21, 61, 61, 61, 89, 89, 61, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 89 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 268 number of broken/clashed sets: 89 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220227 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220227 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220227/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220227 Building REAL300000220228 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220228' /scratch/stefan/7769890/working/building/REAL300000220228 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220228 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220228/0 /scratch/stefan/7769890/working/building/REAL300000220228 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/229 `/scratch/stefan/7769890/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C2=C(C=CC=C2)C2=C1C=CC(C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)=C2) `REAL300000220228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220228 none CCN1C2=C(C=CC=C2)C2=C1C=CC(C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)=C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [45, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 26, 45, 45, 45, 45, 45, 26, 26, 26, 26, 26, 26, 10, 10, 3, 3, 2, 2, 2, 1, 26] 65 rigid atoms, others: [47, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48]) total number of confs: 183 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: REAL300000220228 none CCN1C2=C(C=CC=C2)C2=C1C=CC(C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)=C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 49, 65, 65, 26, 26, 26, 1, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 49, 49, 26, 26, 26, 26, 1] 65 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 34, 35, 36, 37, 38, 39, 48] set([0, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 253 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220228 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220228 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220228/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220228 Building REAL300000220229 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220229' /scratch/stefan/7769890/working/building/REAL300000220229 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220229 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220229/0 /scratch/stefan/7769890/working/building/REAL300000220229 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/230 `/scratch/stefan/7769890/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(COC2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=C2)C=C1) `REAL300000220229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220229 none CC1=CC=C(COC2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 37, 37, 37, 37, 37, 63, 79, 79, 37, 37, 37, 1, 1, 14, 14, 15, 15, 15, 14, 14, 5, 5, 1, 1, 5, 5, 37, 37, 37, 63, 63, 37, 1, 1, 14, 14] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 46, 47, 25, 26, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 333 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220229 none CC1=CC=C(COC2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 59, 59, 154, 154, 154, 154, 154, 201, 201, 201, 154, 154, 154, 17, 17, 1, 1, 2, 2, 2, 1, 1, 7, 7, 17, 17, 59, 59, 154, 154, 154, 201, 201, 154, 17, 17, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 48, 49, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 577 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220229 none CC1=CC=C(COC2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 136, 155, 155, 110, 37, 37, 37, 37, 37, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 37, 37, 155, 155, 155, 155, 155, 155, 155, 110, 110, 37, 37, 12, 12, 2, 2, 2, 3, 3, 1, 37, 37, 155, 155] 201 rigid atoms, others: [45, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 571 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220229 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220229 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220229/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220229 Building REAL300000220230 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220230' /scratch/stefan/7769890/working/building/REAL300000220230 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220230 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220230/0 /scratch/stefan/7769890/working/building/REAL300000220230 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/231 `/scratch/stefan/7769890/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)C=C2)=N1) `REAL300000220230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220230 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 15, 15, 15, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 10, 10, 10, 15, 15, 10, 4, 4, 1, 1, 1, 1] 15 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 53 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: REAL300000220230 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 3, 3, 1, 7, 7, 10, 10, 10, 10] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 44 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220230 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220230 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220230/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220230 Building REAL300000220231 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220231' /scratch/stefan/7769890/working/building/REAL300000220231 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220231 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220231/0 /scratch/stefan/7769890/working/building/REAL300000220231 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/232 `/scratch/stefan/7769890/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)C(=O)N(C)C2=O)=N1) `REAL300000220231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220231 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)C(=O)N(C)C2=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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: [37, 37, 37, 37, 49, 49, 49, 37, 37, 37, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 49, 49, 37, 10, 10, 1, 2, 2, 2, 1, 1, 1] 49 rigid atoms, others: [32, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 134 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: REAL300000220231 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)C(=O)N(C)C2=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 37, 37, 37, 37, 25, 37, 37, 37, 37, 1, 2, 2, 2, 3, 3, 1, 11, 11, 37, 37, 37, 37, 37, 37, 37] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220231 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220231 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220231/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220231 Building REAL300000220232 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220232' /scratch/stefan/7769890/working/building/REAL300000220232 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220232 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220232/0 /scratch/stefan/7769890/working/building/REAL300000220232 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/233 `/scratch/stefan/7769890/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220232 none CC1=NN(C)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 41, 41, 41, 41, 41, 41, 12, 12, 2, 2, 2, 3, 3, 1] 51 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 87 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: REAL300000220232 none CC1=NN(C)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 41, 41, 41, 41, 41, 51, 51, 51, 41, 41, 41, 2, 2, 2, 2, 2, 2, 11, 11, 41, 41, 41, 51, 51, 41] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 133 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220232 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220232 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220232/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220232 Building REAL300000220233 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220233' /scratch/stefan/7769890/working/building/REAL300000220233 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220233 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220233/0 /scratch/stefan/7769890/working/building/REAL300000220233 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/234 `/scratch/stefan/7769890/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(O)C=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220233 none COC1=C(O)C=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [72, 56, 56, 56, 56, 56, 56, 56, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 72, 72, 72, 112, 56, 56, 56, 11, 11, 3, 3, 2, 2, 2, 1] 184 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 246 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: REAL300000220233 none COC1=C(O)C=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 56, 56, 56, 56, 56, 83, 92, 92, 56, 56, 56, 5, 5, 5, 2, 1, 1, 1, 11, 11, 83, 83, 56, 56, 56, 55] 184 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([0, 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]) total number of confs: 290 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220233 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220233 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220233/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220233 Building REAL300000220234 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220234' /scratch/stefan/7769890/working/building/REAL300000220234 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220234 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220234/0 /scratch/stefan/7769890/working/building/REAL300000220234 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/235 `/scratch/stefan/7769890/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220234 none COC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 61, 61, 61, 61, 61, 105, 160, 160, 61, 61, 61, 11, 11, 11, 11, 11, 11, 11, 1, 1, 11, 11, 105, 105, 62, 62, 62, 61, 11, 11] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 33] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 601 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220234 none COC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 52, 52, 133, 133, 133, 133, 133, 201, 201, 201, 133, 133, 133, 1, 1, 2, 2, 2, 1, 1, 11, 11, 52, 52, 201, 201, 133, 133, 133, 133, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 43, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 638 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220234 none COC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 94, 90, 133, 133, 62, 61, 61, 61, 61, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 133, 133, 133, 133, 133, 133, 133, 61, 61, 11, 11, 3, 3, 2, 2, 2, 1, 133, 133] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 388 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220234 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220234 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220234/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220234 Building REAL300000220235 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220235' /scratch/stefan/7769890/working/building/REAL300000220235 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220235 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220235/0 /scratch/stefan/7769890/working/building/REAL300000220235 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/236 `/scratch/stefan/7769890/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220235 none CC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 87, 87, 87, 87, 87, 134, 163, 163, 87, 88, 87, 7, 7, 7, 7, 7, 7, 7, 1, 1, 11, 11, 134, 134, 88, 88, 88, 87, 7, 7] 164 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 527 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: REAL300000220235 none CC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 40, 40, 126, 126, 126, 126, 126, 164, 164, 164, 126, 126, 126, 1, 1, 2, 2, 2, 1, 1, 8, 8, 40, 40, 164, 164, 126, 126, 126, 126, 1, 1] 164 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 42, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 437 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: REAL300000220235 none CC1=CC=C(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [126, 119, 126, 126, 88, 87, 87, 87, 87, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 126, 126, 126, 126, 126, 126, 126, 87, 87, 12, 12, 3, 3, 2, 2, 2, 1, 126, 126] 164 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 237 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220235 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220235 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220235/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220235 Building REAL300000220236 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220236' /scratch/stefan/7769890/working/building/REAL300000220236 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220236 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220236/0 /scratch/stefan/7769890/working/building/REAL300000220236 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/237 `/scratch/stefan/7769890/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC3=CC=CC=C23)N1) `REAL300000220236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220236 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [41, 41, 41, 41, 51, 51, 51, 41, 41, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 51, 51, 11, 11, 1, 1, 1, 1, 1, 41] 51 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 122 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: REAL300000220236 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 3, 3, 11, 11, 41, 41, 41, 41, 41, 1] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220236 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220236 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220236/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220236 Building REAL300000220237 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220237' /scratch/stefan/7769890/working/building/REAL300000220237 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220237 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220237/0 /scratch/stefan/7769890/working/building/REAL300000220237 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/238 `/scratch/stefan/7769890/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C) `REAL300000220237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220237 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [40, 11, 11, 29, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 29, 29, 40, 40, 40, 29, 29, 11, 11, 3, 3, 1, 1, 1, 1, 29, 29, 29, 29] 59 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 138 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: REAL300000220237 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 50, 59, 59, 29, 29, 29, 1, 1, 1, 4, 4, 4, 1, 1, 6, 6, 50, 50, 29, 29, 29, 29, 1, 2, 2, 2] 59 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 217 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220237 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220237 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220237/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220237 Building REAL300000220238 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220238' /scratch/stefan/7769890/working/building/REAL300000220238 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220238 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220238/0 /scratch/stefan/7769890/working/building/REAL300000220238 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/239 `/scratch/stefan/7769890/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N=C3C(=C2)C=NN3C(C)C)=N1) `REAL300000220238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220238 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N=C3C(=C2)C=NN3C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [67, 67, 67, 67, 101, 120, 120, 67, 67, 67, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 67, 101, 101, 67, 9, 9, 1, 1, 12, 13, 13, 13, 13, 13, 13] 133 rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 413 number of broken/clashed sets: 133 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220238 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N=C3C(=C2)C=NN3C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 103, 103, 1, 2, 2, 2, 3, 3, 1, 12, 12, 67, 67, 103, 103, 103, 103, 103, 103, 103] 133 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 310 number of broken/clashed sets: 133 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220238 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220238 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220238/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220238 Building REAL300000220239 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220239' /scratch/stefan/7769890/working/building/REAL300000220239 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220239 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220239/0 /scratch/stefan/7769890/working/building/REAL300000220239 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/240 `/scratch/stefan/7769890/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=CC(Cl)=C2Cl)=N1) `REAL300000220239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220239 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=CC(Cl)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [41, 41, 41, 41, 49, 49, 49, 41, 41, 41, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 49, 49, 41, 7, 7, 1, 1] 49 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 103 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: REAL300000220239 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=CC(Cl)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 3, 3, 1, 11, 11, 41, 41] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 86 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220239 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220239 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220239/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220239 Building REAL300000220240 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220240' /scratch/stefan/7769890/working/building/REAL300000220240 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220240 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220240/0 /scratch/stefan/7769890/working/building/REAL300000220240 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/241 `/scratch/stefan/7769890/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=C(F)C=C3)S2)N1) `REAL300000220240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220240 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=C(F)C=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [44, 44, 44, 44, 53, 55, 55, 44, 44, 44, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 3, 2, 7, 7, 1, 44, 44, 44, 44, 53, 53, 12, 12, 1, 1, 7, 7, 7, 7, 44] 93 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 145 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220240 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=C(F)C=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 44, 44, 44, 44, 82, 82, 74, 75, 82, 82, 44, 1, 2, 2, 2, 3, 3, 11, 11, 44, 44, 82, 82, 82, 82, 1] 93 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 39] set([4, 5, 6, 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: 184 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220240 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=C(F)C=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [82, 82, 82, 82, 93, 93, 93, 82, 82, 82, 45, 45, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 82, 82, 82, 82, 93, 93, 45, 45, 7, 7, 1, 1, 1, 1, 82] 93 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 219 number of broken/clashed sets: 92 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220240 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220240 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220240/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220240 Building REAL300000220241 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220241' /scratch/stefan/7769890/working/building/REAL300000220241 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220241 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220241/0 /scratch/stefan/7769890/working/building/REAL300000220241 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/242 `/scratch/stefan/7769890/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CC=N2)=N1) `REAL300000220241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220241 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CC=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 36, 58, 58, 28, 28, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 54, 54, 54, 54, 54, 28, 28, 28, 28, 36, 36, 28, 7, 7, 1, 1, 1, 1, 23, 23, 54, 54, 54, 54] 201 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45]) total number of confs: 289 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220241 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CC=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 28, 28, 20, 28, 28, 28, 59, 137, 177, 177, 177, 177, 177, 1, 2, 2, 2, 3, 3, 1, 9, 9, 28, 28, 28, 28, 137, 137, 177, 177, 177, 177] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 568 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220241 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CC=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 177, 201, 201, 201, 177, 177, 177, 102, 102, 54, 54, 54, 40, 54, 54, 31, 7, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 201, 201, 177, 102, 102, 54, 54, 54, 54, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 581 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220241 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220241 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220241/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220241 Building REAL300000220242 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220242' /scratch/stefan/7769890/working/building/REAL300000220242 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220242 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220242/0 /scratch/stefan/7769890/working/building/REAL300000220242 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/243 `/scratch/stefan/7769890/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)S2)=N1) `REAL300000220242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220242 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [26, 26, 26, 26, 31, 31, 31, 26, 26, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 31, 31, 26, 9, 9, 1, 1] 31 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 73 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: REAL300000220242 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 26, 26, 26, 26, 26, 1, 2, 2, 2, 3, 3, 1, 9, 9, 26, 26] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 68 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220242 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220242 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220242/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220242 Building REAL300000220243 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220243' /scratch/stefan/7769890/working/building/REAL300000220243 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220243 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220243/0 /scratch/stefan/7769890/working/building/REAL300000220243 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/244 `/scratch/stefan/7769890/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CSC=N2)=N1) `REAL300000220243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220243 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CSC=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 52, 82, 82, 36, 36, 36, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 44, 44, 44, 44, 36, 36, 36, 36, 52, 52, 36, 9, 9, 1, 1, 1, 1, 23, 23, 44, 44] 201 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 368 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220243 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CSC=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 36, 36, 20, 36, 36, 36, 57, 136, 162, 162, 162, 162, 1, 2, 2, 2, 3, 3, 1, 9, 9, 36, 36, 36, 36, 136, 136, 162, 162] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 558 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220243 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CSC=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 14, 1, 8, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 162, 201, 201, 201, 162, 162, 162, 88, 88, 44, 44, 44, 37, 44, 44, 22, 5, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 201, 201, 162, 88, 88, 44, 44, 44, 44, 5, 5, 1, 1] 201 rigid atoms, others: [41, 42, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 580 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220243 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220243 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220243/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220243 Building REAL300000220244 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220244' /scratch/stefan/7769890/working/building/REAL300000220244 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220244 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220244/0 /scratch/stefan/7769890/working/building/REAL300000220244 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/245 `/scratch/stefan/7769890/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CC=N3)C=C2)N1) `REAL300000220244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220244 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CC=N3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 13, 13, 13, 13, 25, 25, 3, 3, 1, 1, 3, 3, 3, 1, 1, 13] 25 rigid atoms, others: [32, 33, 37, 38, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39]) total number of confs: 99 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: REAL300000220244 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CC=N3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 3, 3, 1, 1, 1, 1, 1, 9, 9, 13, 13, 9, 9, 25, 25, 25, 25, 13, 13, 1, 2, 2, 2, 3, 3, 9, 9, 13, 13, 25, 25, 25, 13, 13, 1] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 76 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220244 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CC=N3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 25, 25, 25, 25, 25, 25, 25, 5, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 25, 25, 25, 25, 25, 25, 5, 5, 3, 3, 1, 1, 1, 3, 3, 25] 25 rigid atoms, others: [34, 35, 36, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 50 number of broken/clashed sets: 25 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220244 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220244 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220244/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220244 Building REAL300000220245 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220245' /scratch/stefan/7769890/working/building/REAL300000220245 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220245 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220245/0 /scratch/stefan/7769890/working/building/REAL300000220245 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/246 `/scratch/stefan/7769890/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)S2)=N1) `REAL300000220245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220245 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 77, 83, 83, 53, 53, 53, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 7, 7, 1, 53, 53, 53, 53, 77, 77, 53, 12, 12, 1, 1, 7, 7, 7, 7] 112 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 261 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: REAL300000220245 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 53, 53, 53, 53, 84, 84, 80, 84, 84, 84, 84, 84, 53, 1, 2, 2, 2, 3, 3, 1, 12, 12, 53, 53, 84, 84, 84, 84] 112 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 175 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220245 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C([N+](=O)[O-])C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 112, 112, 112, 84, 84, 84, 38, 38, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 84, 84, 84, 84, 112, 112, 84, 38, 38, 7, 7, 1, 1, 1, 1] 112 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 322 number of broken/clashed sets: 111 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220245 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220245 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220245/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220245 Building REAL300000220246 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220246' /scratch/stefan/7769890/working/building/REAL300000220246 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220246 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220246/0 /scratch/stefan/7769890/working/building/REAL300000220246 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/247 `/scratch/stefan/7769890/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)S2)=N1) `REAL300000220246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220246 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [55, 55, 55, 55, 89, 102, 102, 55, 55, 55, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 1, 55, 55, 55, 55, 89, 89, 55, 12, 11, 1, 1, 7, 7, 2, 7] 138 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 352 number of broken/clashed sets: 137 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220246 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 55, 55, 55, 55, 111, 111, 92, 111, 111, 111, 55, 1, 2, 2, 2, 3, 3, 1, 11, 11, 55, 55, 111, 111, 95, 111] 138 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 255 number of broken/clashed sets: 137 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220246 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC=C3Cl)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [111, 111, 111, 111, 138, 138, 138, 111, 111, 111, 47, 47, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 111, 111, 111, 111, 138, 138, 111, 47, 47, 7, 7, 1, 1, 1, 1] 138 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 359 number of broken/clashed sets: 137 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220246 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220246 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220246/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220246 Building REAL300000220247 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220247' /scratch/stefan/7769890/working/building/REAL300000220247 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220247 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220247/0 /scratch/stefan/7769890/working/building/REAL300000220247 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/248 `/scratch/stefan/7769890/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)S2)=N1) `REAL300000220247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220247 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [50, 50, 50, 50, 74, 103, 103, 51, 51, 51, 9, 9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 1, 50, 51, 51, 51, 74, 74, 51, 10, 9, 1, 1, 12, 12, 12, 12] 201 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 351 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220247 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 170, 170, 170, 170, 170, 170, 170, 170, 50, 1, 2, 2, 2, 3, 3, 1, 9, 9, 50, 50, 170, 170, 170, 170] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 245 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220247 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC([N+](=O)[O-])=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [170, 170, 170, 170, 201, 201, 201, 170, 170, 170, 65, 65, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 170, 170, 170, 170, 201, 201, 170, 65, 65, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 475 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220247 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220247 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220247/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220247 Building REAL300000220248 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220248' /scratch/stefan/7769890/working/building/REAL300000220248 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220248 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220248/0 /scratch/stefan/7769890/working/building/REAL300000220248 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/249 `/scratch/stefan/7769890/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)S2)N1) `REAL300000220248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220248 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 69, 69, 69, 99, 109, 109, 69, 69, 69, 11, 11, 1, 1, 1, 1, 1, 1, 13, 13, 1, 13, 13, 13, 1, 69, 70, 70, 70, 99, 99, 11, 11, 1, 1, 13, 13, 10, 13, 70] 201 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 350 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220248 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 69, 69, 69, 69, 156, 156, 74, 156, 156, 156, 69, 1, 2, 2, 2, 3, 3, 11, 11, 69, 69, 156, 156, 154, 156, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 39] set([4, 5, 6, 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: 491 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220248 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3F)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 156, 201, 201, 201, 156, 156, 156, 86, 86, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 156, 156, 156, 156, 201, 201, 86, 86, 13, 13, 1, 1, 1, 1, 156] 201 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 558 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220248 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220248 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220248/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220248 Building REAL300000220249 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220249' /scratch/stefan/7769890/working/building/REAL300000220249 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220249 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220249/0 /scratch/stefan/7769890/working/building/REAL300000220249 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/250 `/scratch/stefan/7769890/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220249 none CNC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [39, 39, 21, 39, 11, 34, 34, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 34, 34, 39, 39, 39, 39, 34, 34, 11, 11, 3, 3, 2, 2, 2, 1, 34, 34] 49 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 207 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: REAL300000220249 none CNC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [4, 4, 1, 4, 1, 1, 1, 1, 1, 6, 6, 34, 34, 34, 34, 34, 49, 49, 49, 34, 34, 34, 1, 1, 4, 4, 4, 4, 1, 1, 6, 6, 49, 49, 34, 34, 34, 34, 1, 1] 49 rigid atoms, others: [2, 4, 5, 6, 7, 8, 39, 22, 23, 38, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 145 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220249 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220249 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220249/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220249 Building REAL300000220250 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220250' /scratch/stefan/7769890/working/building/REAL300000220250 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220250 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220250/0 /scratch/stefan/7769890/working/building/REAL300000220250 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/251 `/scratch/stefan/7769890/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(Br)=C2)=N1) `REAL300000220250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220250 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [23, 23, 23, 23, 29, 29, 29, 23, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 29, 29, 23, 7, 7, 1, 1] 29 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 73 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: REAL300000220250 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 3, 1, 9, 9, 23, 23] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 62 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220250 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220250 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220250/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220250 Building REAL300000220251 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220251' /scratch/stefan/7769890/working/building/REAL300000220251 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220251 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220251/0 /scratch/stefan/7769890/working/building/REAL300000220251 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/252 `/scratch/stefan/7769890/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC(Cl)=C3)S2)=N1) `REAL300000220251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220251 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC(Cl)=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 64, 94, 106, 106, 64, 64, 64, 11, 11, 1, 1, 1, 1, 1, 1, 12, 12, 11, 12, 12, 12, 1, 64, 64, 64, 64, 94, 94, 64, 11, 11, 1, 1, 12, 12, 11, 12] 201 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 330 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220251 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC(Cl)=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 64, 64, 64, 64, 172, 172, 172, 172, 172, 172, 64, 1, 2, 2, 2, 3, 3, 1, 11, 11, 64, 64, 172, 172, 172, 172] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 258 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220251 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC(Cl)=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 172, 201, 201, 201, 172, 172, 172, 72, 72, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 172, 172, 172, 172, 201, 201, 172, 72, 72, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 470 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220251 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220251 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220251/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220251 Building REAL300000220252 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220252' /scratch/stefan/7769890/working/building/REAL300000220252 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220252 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220252/0 /scratch/stefan/7769890/working/building/REAL300000220252 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/253 `/scratch/stefan/7769890/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCCC(=O)[O-])C=C2)=N1) `REAL300000220252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220252 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCCC(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 35, 56, 56, 21, 21, 21, 3, 3, 1, 1, 1, 1, 1, 1, 7, 11, 31, 37, 37, 1, 1, 21, 21, 21, 21, 35, 35, 21, 3, 3, 1, 1, 11, 11, 31, 31, 1, 1] 201 rigid atoms, others: [34, 35, 40, 41, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 340 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220252 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCCC(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 21, 21, 12, 12, 89, 107, 157, 162, 162, 21, 21, 1, 2, 2, 2, 3, 3, 1, 12, 12, 21, 21, 107, 107, 157, 157, 21, 21] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 583 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220252 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220252 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220252/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220252 Building REAL300000220253 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220253' /scratch/stefan/7769890/working/building/REAL300000220253 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220253 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220253/0 /scratch/stefan/7769890/working/building/REAL300000220253 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/254 `/scratch/stefan/7769890/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC(C3=CC=CC=N3)=N2)N1) `REAL300000220253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220253 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC(C3=CC=CC=N3)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [63, 63, 63, 63, 93, 123, 123, 62, 63, 62, 13, 13, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 63, 63, 63, 63, 93, 93, 13, 13, 1, 12, 12, 12, 12, 63] 160 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 398 number of broken/clashed sets: 159 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220253 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC(C3=CC=CC=N3)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 63, 63, 63, 63, 133, 133, 133, 133, 133, 63, 1, 2, 2, 2, 3, 3, 11, 11, 63, 133, 133, 133, 133, 1] 160 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 209 number of broken/clashed sets: 159 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220253 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC(C3=CC=CC=N3)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [133, 133, 133, 133, 160, 160, 160, 133, 133, 133, 55, 55, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 133, 133, 133, 133, 160, 160, 55, 55, 12, 1, 1, 1, 1, 133] 160 rigid atoms, others: [33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 401 number of broken/clashed sets: 159 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220253 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220253 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220253/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220253 Building REAL300000220254 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220254' /scratch/stefan/7769890/working/building/REAL300000220254 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220254 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220254/0 /scratch/stefan/7769890/working/building/REAL300000220254 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/255 `/scratch/stefan/7769890/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3CCCC3)C=C2)N1) `REAL300000220254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220254 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3CCCC3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 16, 16, 26, 28, 28, 16, 16, 16, 4, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 16, 16, 16, 16, 26, 26, 4, 4, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 16] 51 rigid atoms, others: [32, 33, 42, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 98 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220254 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3CCCC3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 16, 16, 11, 13, 39, 39, 39, 39, 16, 16, 1, 2, 2, 2, 3, 3, 11, 11, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 16, 16, 1] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 44, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220254 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3CCCC3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 39, 39, 39, 51, 51, 51, 39, 39, 39, 11, 11, 1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 39, 39, 39, 39, 51, 51, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 39] 51 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 51 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220254 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220254 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220254/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220254 Building REAL300000220255 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220255' /scratch/stefan/7769890/working/building/REAL300000220255 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220255 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220255/0 /scratch/stefan/7769890/working/building/REAL300000220255 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/256 `/scratch/stefan/7769890/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220255 none CCCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 131, 131, 131, 131, 54, 54, 13, 13, 23, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 23, 23, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 54, 54, 23, 23, 8, 8, 2, 2, 2, 3, 3, 1, 23, 23] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 52, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 498 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220255 none CCCCCCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 23, 23, 23, 23, 23, 41, 56, 56, 23, 23, 23, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 1, 5, 5, 23, 23, 23, 41, 41, 23, 1, 1] 201 rigid atoms, others: [11, 7, 8, 9, 10, 43, 44, 12, 53, 54, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 232 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220255 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220255 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220255/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220255 Building REAL300000220256 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220256' /scratch/stefan/7769890/working/building/REAL300000220256 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220256 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220256/0 /scratch/stefan/7769890/working/building/REAL300000220256 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/257 `/scratch/stefan/7769890/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=CC=C2F)N1) `REAL300000220256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220256 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [28, 28, 28, 28, 44, 44, 44, 28, 28, 28, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 44, 44, 9, 9, 1, 1, 1, 28] 44 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 140 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: REAL300000220256 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 28, 28, 28, 28, 28, 28, 28, 1, 2, 2, 2, 3, 3, 11, 11, 28, 28, 28, 1] 44 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220256 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220256 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220256/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220256 Building REAL300000220257 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220257' /scratch/stefan/7769890/working/building/REAL300000220257 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220257 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220257/0 /scratch/stefan/7769890/working/building/REAL300000220257 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/258 `/scratch/stefan/7769890/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(OC(C)C)C=C2)N1) `REAL300000220257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220257 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(OC(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 27, 27, 27, 44, 72, 72, 27, 27, 27, 4, 4, 1, 1, 1, 1, 1, 1, 13, 35, 35, 1, 1, 27, 27, 27, 27, 44, 44, 4, 4, 1, 1, 35, 35, 35, 35, 35, 35, 35, 1, 1, 27] 140 rigid atoms, others: [32, 40, 41, 12, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 354 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220257 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(OC(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 27, 27, 12, 12, 95, 116, 116, 27, 27, 1, 2, 2, 2, 3, 3, 12, 12, 27, 27, 116, 116, 116, 116, 116, 116, 116, 27, 27, 1] 140 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 42] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 336 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220257 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220257 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220257/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220257 Building REAL300000220258 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220258' /scratch/stefan/7769890/working/building/REAL300000220258 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220258 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220258/0 /scratch/stefan/7769890/working/building/REAL300000220258 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/259 `/scratch/stefan/7769890/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C12) `REAL300000220258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220258 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [82, 55, 55, 55, 55, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 55, 55, 55, 55, 55, 55, 82, 82, 82, 55, 55, 12, 12, 3, 3, 2, 2, 2, 1, 55, 55, 55, 55] 96 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 157 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: REAL300000220258 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 10, 10, 55, 55, 55, 55, 55, 84, 96, 96, 55, 55, 55, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 10, 10, 84, 84, 55, 55, 55, 55, 1, 1, 1, 1] 96 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 41, 42, 20, 21, 22, 23, 24, 25, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 305 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220258 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220258 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220258/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220258 Building REAL300000220259 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220259' /scratch/stefan/7769890/working/building/REAL300000220259 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220259 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220259/0 /scratch/stefan/7769890/working/building/REAL300000220259 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/260 `/scratch/stefan/7769890/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CN=C2)=N1) `REAL300000220259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220259 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CN=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 37, 62, 62, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 25, 56, 56, 56, 56, 56, 31, 31, 31, 31, 37, 37, 31, 7, 7, 1, 1, 1, 1, 25, 25, 56, 56, 56, 56] 201 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45]) total number of confs: 300 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220259 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CN=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 31, 31, 19, 31, 31, 31, 55, 151, 178, 178, 178, 178, 178, 1, 2, 2, 2, 3, 3, 1, 9, 9, 31, 31, 31, 31, 151, 151, 178, 178, 178, 178] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 603 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220259 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC2=CC=CN=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 178, 201, 201, 201, 178, 178, 178, 93, 93, 56, 56, 56, 56, 56, 56, 33, 7, 1, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 201, 201, 178, 93, 93, 56, 56, 56, 56, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 503 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220259 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220259 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220259/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220259 Building REAL300000220260 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220260' /scratch/stefan/7769890/working/building/REAL300000220260 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220260 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220260/0 /scratch/stefan/7769890/working/building/REAL300000220260 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/261 `/scratch/stefan/7769890/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OC(F)F)=N1) `REAL300000220260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220260 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OC(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 97, 139, 139, 59, 59, 59, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 39, 39, 59, 59, 59, 59, 97, 97, 59, 9, 9, 1, 1, 1, 39] 201 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 596 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220260 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OC(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 59, 59, 59, 17, 59, 59, 59, 140, 185, 185, 1, 2, 2, 2, 3, 3, 1, 11, 11, 59, 59, 59, 185] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 611 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220260 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220260 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220260/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220260 Building REAL300000220261 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220261' /scratch/stefan/7769890/working/building/REAL300000220261 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220261 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220261/0 /scratch/stefan/7769890/working/building/REAL300000220261 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/262 `/scratch/stefan/7769890/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2N2C=NC=N2)N1) `REAL300000220261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220261 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2N2C=NC=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 101, 130, 130, 56, 56, 56, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 56, 56, 56, 56, 101, 101, 9, 9, 1, 1, 1, 1, 10, 10, 55] 163 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 470 number of broken/clashed sets: 162 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220261 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2N2C=NC=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 56, 56, 24, 56, 56, 56, 105, 105, 105, 105, 1, 2, 2, 2, 3, 3, 12, 12, 56, 56, 56, 56, 105, 105, 1] 163 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 313 number of broken/clashed sets: 162 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220261 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2N2C=NC=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 163, 163, 163, 105, 105, 105, 35, 35, 10, 10, 10, 9, 10, 10, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 163, 163, 35, 35, 10, 10, 10, 10, 1, 1, 105] 163 rigid atoms, others: [36, 37, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 525 number of broken/clashed sets: 162 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220261 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220261 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220261/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220261 Building REAL300000220262 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220262' /scratch/stefan/7769890/working/building/REAL300000220262 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220262 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220262/0 /scratch/stefan/7769890/working/building/REAL300000220262 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/263 `/scratch/stefan/7769890/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)O2)C=C1) `REAL300000220262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220262 none CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 67, 67, 93, 117, 117, 67, 67, 67, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 12, 12, 93, 93, 68, 68, 68, 67, 7, 7] 122 rigid atoms, others: [4, 5, 6, 7, 8, 9, 32, 23, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 383 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220262 none CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 57, 57, 106, 106, 106, 106, 106, 122, 122, 122, 106, 106, 106, 8, 1, 1, 2, 2, 2, 1, 1, 8, 8, 57, 57, 122, 122, 106, 106, 106, 106, 1, 1] 122 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 42, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 298 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: REAL300000220262 none CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 103, 103, 67, 67, 67, 67, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 67, 103, 103, 103, 103, 103, 103, 103, 67, 68, 11, 11, 3, 3, 2, 2, 2, 1, 103, 103] 122 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 413 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220262 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220262 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220262/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220262 Building REAL300000220263 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220263' /scratch/stefan/7769890/working/building/REAL300000220263 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220263 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220263/0 /scratch/stefan/7769890/working/building/REAL300000220263 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/264 `/scratch/stefan/7769890/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC(F)(F)F)=C2)=N1) `REAL300000220263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220263 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 60, 74, 74, 37, 37, 37, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 1, 37, 37, 37, 37, 60, 60, 37, 6, 6, 1, 1, 1, 15, 15, 1] 201 rigid atoms, others: [34, 35, 36, 39, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 290 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220263 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 37, 37, 37, 37, 37, 106, 141, 141, 141, 141, 37, 1, 2, 2, 2, 3, 3, 1, 10, 10, 37, 37, 37, 141, 141, 37] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 375 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220263 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220263 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220263/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220263 Building REAL300000220264 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220264' /scratch/stefan/7769890/working/building/REAL300000220264 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220264 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220264/0 /scratch/stefan/7769890/working/building/REAL300000220264 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/265 `/scratch/stefan/7769890/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCO3)N1) `REAL300000220264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220264 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCO3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [38, 38, 38, 38, 50, 50, 50, 38, 38, 38, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 50, 50, 12, 12, 1, 1, 1, 1, 1, 38] 50 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 131 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: REAL300000220264 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCO3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 38, 38, 38, 38, 38, 38, 38, 38, 1, 2, 2, 2, 3, 3, 11, 11, 38, 38, 38, 38, 38, 1] 50 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220264 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220264 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220264/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220264 Building REAL300000220265 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220265' /scratch/stefan/7769890/working/building/REAL300000220265 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220265 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220265/0 /scratch/stefan/7769890/working/building/REAL300000220265 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/266 `/scratch/stefan/7769890/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(Cl)C=C3)N=C2)=N1) `REAL300000220265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220265 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(Cl)C=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 27, 27, 39, 39, 39, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 4, 1, 1, 27, 27, 27, 27, 39, 39, 27, 7, 7, 1, 4, 4, 4, 4, 1] 39 rigid atoms, others: [34, 39, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 124 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: REAL300000220265 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(Cl)C=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 27, 27, 27, 31, 31, 27, 31, 31, 31, 27, 27, 1, 2, 2, 2, 3, 3, 1, 10, 10, 27, 31, 31, 31, 31, 27] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 97 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220265 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(Cl)C=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 39, 39, 39, 31, 31, 31, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 31, 31, 31, 31, 39, 39, 31, 10, 10, 4, 1, 1, 1, 1, 4] 39 rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 98 number of broken/clashed sets: 38 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220265 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220265 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220265/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220265 Building REAL300000220266 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220266' /scratch/stefan/7769890/working/building/REAL300000220266 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220266 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220266/0 /scratch/stefan/7769890/working/building/REAL300000220266 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/267 `/scratch/stefan/7769890/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220266 none CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 117, 48, 48, 48, 48, 48, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 48, 159, 159, 159, 159, 159, 48, 48, 48, 12, 12, 3, 3, 2, 2, 2, 1, 48] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 434 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: REAL300000220266 none CCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 48, 48, 48, 48, 48, 80, 114, 114, 48, 48, 48, 1, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 80, 80, 48, 48, 48, 48, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 39, 22, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 446 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220266 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220266 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220266/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220266 Building REAL300000220267 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220267' /scratch/stefan/7769890/working/building/REAL300000220267 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220267 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220267/0 /scratch/stefan/7769890/working/building/REAL300000220267 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/268 `/scratch/stefan/7769890/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC([N+](=O)[O-])=C2)=N1) `REAL300000220267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220267 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [22, 22, 22, 22, 33, 33, 33, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 22, 22, 22, 33, 33, 22, 6, 6, 1, 1] 33 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 105 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: REAL300000220267 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 3, 6, 6, 1, 1, 1, 1, 1, 8, 8, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 1, 8, 8, 22, 22] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 63 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220267 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220267 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220267/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220267 Building REAL300000220268 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220268' /scratch/stefan/7769890/working/building/REAL300000220268 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220268 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220268/0 /scratch/stefan/7769890/working/building/REAL300000220268 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/269 `/scratch/stefan/7769890/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220268 none COC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 11, 10, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 34, 34, 34, 33, 33, 63, 100, 100, 34, 34, 34, 11, 15, 15, 15, 10, 11, 11, 1, 1, 11, 11, 63, 63, 34, 34, 34, 34, 11] 201 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 403 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220268 none COC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 36, 36, 90, 90, 90, 90, 90, 158, 201, 201, 90, 90, 90, 1, 3, 3, 3, 1, 1, 1, 11, 11, 36, 36, 158, 158, 90, 90, 90, 90, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 43, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220268 none COC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 90, 90, 90, 90, 90, 34, 34, 34, 34, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 90, 118, 118, 118, 90, 90, 90, 33, 34, 8, 8, 3, 3, 2, 2, 2, 1, 90] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43]) total number of confs: 207 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220268 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220268 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220268/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220268 Building REAL300000220269 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220269' /scratch/stefan/7769890/working/building/REAL300000220269 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220269 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220269/0 /scratch/stefan/7769890/working/building/REAL300000220269 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/270 `/scratch/stefan/7769890/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220269 none COCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 120, 106, 104, 29, 29, 29, 29, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 131, 131, 131, 120, 120, 106, 106, 29, 29, 29, 9, 9, 2, 2, 2, 3, 3, 1, 29] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43]) total number of confs: 279 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220269 none COCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 7, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 54, 78, 78, 29, 29, 29, 1, 24, 24, 24, 12, 12, 7, 7, 1, 1, 1, 5, 5, 29, 29, 29, 54, 54, 29, 1] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 43, 24] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 339 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220269 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220269 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220269/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220269 Building REAL300000220270 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220270' /scratch/stefan/7769890/working/building/REAL300000220270 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220270 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220270/0 /scratch/stefan/7769890/working/building/REAL300000220270 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/271 `/scratch/stefan/7769890/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCOCC3)N=C2)=N1) `REAL300000220270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220270 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCOCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 31, 49, 49, 19, 19, 19, 3, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 1, 19, 19, 19, 19, 31, 31, 19, 3, 3, 1, 13, 13, 12, 13, 12, 13, 13, 13, 1] 67 rigid atoms, others: [34, 43, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 189 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: REAL300000220270 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCOCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 19, 19, 9, 9, 60, 60, 60, 60, 60, 19, 19, 1, 2, 2, 2, 3, 3, 1, 9, 9, 19, 60, 60, 60, 60, 60, 60, 60, 60, 19] 67 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 153 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220270 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(N3CCOCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 67, 67, 67, 60, 60, 60, 21, 21, 2, 2, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 60, 60, 60, 60, 67, 67, 60, 21, 21, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13] 67 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43]) total number of confs: 167 number of broken/clashed sets: 66 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220270 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220270 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220270/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220270 Building REAL300000220271 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220271' /scratch/stefan/7769890/working/building/REAL300000220271 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220271 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220271/0 /scratch/stefan/7769890/working/building/REAL300000220271 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/272 `/scratch/stefan/7769890/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)N=C2)N1) `REAL300000220271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220271 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [14, 14, 14, 14, 21, 32, 32, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 14, 14, 14, 14, 21, 21, 3, 3, 1, 7, 7, 1, 7, 7, 1, 14] 32 rigid atoms, others: [33, 39, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 40]) total number of confs: 127 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: REAL300000220271 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 9, 9, 29, 29, 11, 29, 29, 13, 13, 1, 2, 2, 2, 3, 3, 9, 9, 13, 29, 29, 11, 29, 29, 13, 1] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 40, 25] set([4, 5, 6, 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, 39]) total number of confs: 128 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220271 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 32, 32, 32, 31, 31, 31, 11, 11, 1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 31, 31, 31, 32, 32, 11, 11, 7, 1, 1, 1, 1, 1, 7, 31] 32 rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 74 number of broken/clashed sets: 31 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220271 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220271 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220271/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220271 Building REAL300000220272 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220272' /scratch/stefan/7769890/working/building/REAL300000220272 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220272 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220272/0 /scratch/stefan/7769890/working/building/REAL300000220272 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/273 `/scratch/stefan/7769890/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCCCO3)N1) `REAL300000220272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220272 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCCCO3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 50, 50, 50, 35, 35, 35, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 41, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 144 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: REAL300000220272 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCCCO3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1] 50 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 41, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 79 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220272 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220272 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220272/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220272 Building REAL300000220273 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220273' /scratch/stefan/7769890/working/building/REAL300000220273 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220273 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220273/0 /scratch/stefan/7769890/working/building/REAL300000220273 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/274 `/scratch/stefan/7769890/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Cl)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220273 none COC1=CC=C(Cl)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [77, 63, 63, 63, 11, 63, 63, 63, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 77, 77, 77, 63, 63, 63, 11, 11, 3, 3, 2, 2, 2, 1] 98 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 278 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: REAL300000220273 none COC1=CC=C(Cl)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 63, 63, 63, 63, 63, 92, 98, 98, 63, 63, 63, 4, 4, 4, 1, 1, 1, 11, 11, 92, 92, 63, 63, 63, 63] 98 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 292 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220273 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220273 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220273/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220273 Building REAL300000220274 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220274' /scratch/stefan/7769890/working/building/REAL300000220274 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220274 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220274/0 /scratch/stefan/7769890/working/building/REAL300000220274 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/275 `/scratch/stefan/7769890/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(Cl)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220274 none CC1=NN(C2=CC=C(Cl)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 24, 24, 73, 73, 73, 73, 73, 98, 98, 98, 73, 73, 73, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 24, 24, 73, 73, 73, 98, 98, 73] 98 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 267 number of broken/clashed sets: 97 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220274 none CC1=NN(C2=CC=C(Cl)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 6, 6, 2, 2, 6, 6, 1, 1, 1, 1, 9, 9, 43, 43, 43, 43, 43, 67, 94, 94, 43, 43, 43, 2, 2, 2, 6, 6, 6, 6, 2, 2, 2, 9, 9, 43, 43, 43, 67, 67, 43] 98 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 336 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220274 none CC1=NN(C2=CC=C(Cl)C=C2)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 43, 73, 73, 67, 67, 73, 73, 43, 43, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 43, 43, 43, 73, 73, 73, 73, 43, 43, 43, 12, 12, 2, 2, 2, 3, 3, 1] 98 rigid atoms, others: [45, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 97 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220274 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220274 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220274/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220274 Building REAL300000220275 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220275' /scratch/stefan/7769890/working/building/REAL300000220275 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220275 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220275/0 /scratch/stefan/7769890/working/building/REAL300000220275 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/276 `/scratch/stefan/7769890/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220275 none CCCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 68, 68, 20, 20, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 20, 133, 133, 133, 133, 133, 68, 68, 20, 20, 20, 7, 7, 3, 3, 1, 1, 1, 1, 20] 201 rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 475 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: REAL300000220275 none CCCOC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 20, 20, 20, 20, 20, 36, 68, 68, 20, 20, 20, 1, 13, 13, 13, 13, 13, 5, 5, 1, 1, 1, 5, 5, 36, 36, 20, 20, 20, 20, 1] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 42, 23, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 295 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220275 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220275 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220275/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220275 Building REAL300000220276 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220276' /scratch/stefan/7769890/working/building/REAL300000220276 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220276 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220276/0 /scratch/stefan/7769890/working/building/REAL300000220276 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/277 `/scratch/stefan/7769890/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCCC3=C2)N1) `REAL300000220276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220276 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [19, 19, 19, 19, 26, 26, 26, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 26, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 19] 26 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 37]) total number of confs: 73 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: REAL300000220276 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 9, 9, 19, 19, 19, 19, 19, 19, 19, 1] 26 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 59 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220276 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220276 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220276/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220276 Building REAL300000220277 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220277' /scratch/stefan/7769890/working/building/REAL300000220277 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220277 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220277/0 /scratch/stefan/7769890/working/building/REAL300000220277 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/278 `/scratch/stefan/7769890/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CS3)C=C2F)N1) `REAL300000220277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220277 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CS3)C=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 95, 110, 110, 65, 65, 65, 12, 12, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 1, 65, 65, 65, 65, 95, 95, 12, 12, 1, 1, 13, 13, 13, 1, 65] 175 rigid atoms, others: [33, 34, 38, 12, 13, 14, 15, 16, 17, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 39]) total number of confs: 342 number of broken/clashed sets: 175 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220277 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CS3)C=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 65, 65, 65, 65, 155, 155, 155, 155, 65, 65, 65, 1, 2, 2, 2, 3, 3, 11, 11, 65, 65, 155, 155, 155, 65, 1] 175 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 39] set([4, 5, 6, 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: 246 number of broken/clashed sets: 175 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220277 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CS3)C=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 175, 175, 175, 155, 155, 155, 79, 79, 12, 12, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 13, 155, 155, 155, 155, 175, 175, 79, 79, 13, 13, 1, 1, 1, 13, 155] 175 rigid atoms, others: [35, 36, 37, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 416 number of broken/clashed sets: 175 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220277 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220277 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220277/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220277 Building REAL300000220278 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220278' /scratch/stefan/7769890/working/building/REAL300000220278 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220278 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220278/0 /scratch/stefan/7769890/working/building/REAL300000220278 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/279 `/scratch/stefan/7769890/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCCO3)N1) `REAL300000220278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220278 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCCO3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 4, 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: [35, 35, 35, 35, 47, 47, 47, 35, 35, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 47, 47, 11, 11, 1, 1, 1, 1, 1, 1, 1, 35] 47 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 128 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220278 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCCO3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 10, 10, 35, 35, 35, 35, 35, 35, 35, 1] 47 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220278 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220278 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220278/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220278 Building REAL300000220279 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220279' /scratch/stefan/7769890/working/building/REAL300000220279 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220279 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220279/0 /scratch/stefan/7769890/working/building/REAL300000220279 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/280 `/scratch/stefan/7769890/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C3=CC=CC=C3)=CS2)N1) `REAL300000220279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220279 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C3=CC=CC=C3)=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [64, 64, 64, 64, 88, 97, 97, 63, 64, 63, 12, 12, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 64, 64, 64, 64, 88, 88, 12, 12, 1, 3, 3, 2, 3, 3, 1, 64] 97 rigid atoms, others: [32, 38, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 39]) total number of confs: 280 number of broken/clashed sets: 96 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220279 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C3=CC=CC=C3)=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 64, 64, 64, 78, 78, 64, 78, 78, 64, 64, 1, 2, 2, 2, 3, 3, 11, 11, 64, 78, 78, 64, 78, 78, 64, 1] 97 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 183 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220279 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C3=CC=CC=C3)=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [78, 78, 78, 78, 97, 97, 97, 78, 78, 78, 23, 23, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 78, 78, 78, 78, 97, 97, 23, 23, 3, 1, 1, 1, 1, 1, 3, 78] 97 rigid atoms, others: [33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 239 number of broken/clashed sets: 96 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220279 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220279 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220279/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220279 Building REAL300000220280 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220280' /scratch/stefan/7769890/working/building/REAL300000220280 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220280 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220280/0 /scratch/stefan/7769890/working/building/REAL300000220280 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/281 `/scratch/stefan/7769890/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2=CC=CC=C2)N1) `REAL300000220280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220280 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 83, 85, 85, 53, 53, 53, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 53, 53, 53, 53, 83, 83, 9, 9, 1, 1, 1, 1, 4, 4, 4, 4, 4, 53] 85 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 270 number of broken/clashed sets: 85 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220280 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 53, 53, 53, 53, 53, 53, 61, 61, 57, 61, 61, 1, 2, 2, 2, 3, 3, 11, 11, 53, 53, 53, 53, 61, 61, 61, 61, 61, 1] 85 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 42] set([4, 5, 6, 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, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220280 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 85, 85, 85, 61, 61, 61, 19, 19, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 85, 85, 19, 19, 4, 4, 4, 4, 1, 1, 1, 1, 1, 61] 85 rigid atoms, others: [37, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 243 number of broken/clashed sets: 85 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220280 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220280 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220280/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220280 Building REAL300000220281 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220281' /scratch/stefan/7769890/working/building/REAL300000220281 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220281 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220281/0 /scratch/stefan/7769890/working/building/REAL300000220281 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/282 `/scratch/stefan/7769890/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CC=C3)=C2)N1) `REAL300000220281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220281 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CC=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 53, 71, 71, 30, 30, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 30, 30, 30, 30, 53, 53, 6, 6, 1, 1, 1, 3, 3, 1, 3, 3, 1, 30] 71 rigid atoms, others: [33, 34, 35, 41, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 42]) total number of confs: 258 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220281 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CC=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 10, 10, 30, 30, 30, 30, 30, 48, 48, 30, 48, 48, 30, 1, 2, 2, 2, 3, 3, 10, 10, 30, 30, 30, 48, 48, 30, 48, 48, 30, 1] 71 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 42] set([4, 5, 6, 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, 39, 40, 41]) total number of confs: 165 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220281 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CC=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 71, 71, 71, 48, 48, 48, 10, 10, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 48, 48, 48, 48, 71, 71, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 3, 48] 71 rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 206 number of broken/clashed sets: 71 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220281 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220281 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220281/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220281 Building REAL300000220282 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220282' /scratch/stefan/7769890/working/building/REAL300000220282 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220282 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220282/0 /scratch/stefan/7769890/working/building/REAL300000220282 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/283 `/scratch/stefan/7769890/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)O2)N1) `REAL300000220282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220282 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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: [68, 68, 68, 68, 95, 113, 113, 67, 68, 67, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 68, 68, 68, 68, 95, 95, 13, 13, 1, 1, 7, 7, 1, 7, 7, 68] 118 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 345 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220282 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 68, 68, 68, 68, 101, 101, 68, 101, 101, 68, 1, 2, 2, 2, 3, 3, 11, 11, 68, 68, 101, 101, 68, 101, 101, 1] 118 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 271 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220282 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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: [101, 101, 101, 101, 118, 118, 118, 101, 101, 101, 51, 51, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 101, 101, 101, 101, 118, 118, 51, 51, 7, 7, 1, 1, 1, 1, 1, 101] 118 rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 287 number of broken/clashed sets: 117 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220282 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220282 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220282/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220282 Building REAL300000220283 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220283' /scratch/stefan/7769890/working/building/REAL300000220283 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220283 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220283/0 /scratch/stefan/7769890/working/building/REAL300000220283 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/284 `/scratch/stefan/7769890/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC(Cl)=C2)=N1) `REAL300000220283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220283 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 17, 17, 17, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 17, 17, 13, 3, 3, 1, 1, 1] 17 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 43 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: REAL300000220283 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 13, 9, 13, 13, 13, 1, 2, 2, 2, 3, 3, 1, 9, 9, 13, 9, 13] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 62 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220283 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220283 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220283/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220283 Building REAL300000220284 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220284' /scratch/stefan/7769890/working/building/REAL300000220284 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220284 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220284/0 /scratch/stefan/7769890/working/building/REAL300000220284 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/285 `/scratch/stefan/7769890/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3CCCC3)=C2)=N1) `REAL300000220284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220284 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3CCCC3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 47, 57, 57, 25, 25, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 1, 25, 25, 25, 25, 47, 47, 25, 5, 5, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1] 201 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 245 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220284 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3CCCC3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 25, 25, 86, 124, 124, 124, 124, 25, 1, 2, 2, 2, 3, 3, 1, 9, 9, 25, 25, 25, 124, 124, 124, 124, 124, 124, 124, 124, 124, 25] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 294 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220284 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3CCCC3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 124, 201, 201, 201, 124, 124, 124, 48, 48, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 17, 124, 124, 124, 124, 201, 201, 124, 48, 48, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 676 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220284 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220284 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220284/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220284 Building REAL300000220285 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220285' /scratch/stefan/7769890/working/building/REAL300000220285 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220285 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220285/0 /scratch/stefan/7769890/working/building/REAL300000220285 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/286 `/scratch/stefan/7769890/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCN(C)CC3)C(F)=C2)=N1) `REAL300000220285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220285 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCN(C)CC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 15, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 41, 41, 41, 68, 88, 88, 41, 41, 41, 6, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 41, 42, 42, 42, 68, 68, 41, 6, 6, 1, 1, 9, 9, 9, 9, 10, 10, 10, 9, 9, 9, 9, 1] 118 rigid atoms, others: [36, 37, 49, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 314 number of broken/clashed sets: 118 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220285 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCN(C)CC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 15, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 41, 41, 34, 41, 95, 95, 95, 95, 95, 95, 41, 41, 41, 1, 2, 2, 2, 3, 3, 1, 11, 11, 41, 41, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 41] 118 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220285 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCN(C)CC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 15, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 95, 95, 95, 118, 118, 118, 95, 95, 95, 34, 34, 9, 2, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 94, 95, 95, 95, 118, 118, 95, 34, 34, 9, 9, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 9] 118 rigid atoms, others: [48, 38, 39, 40, 41, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 49]) total number of confs: 328 number of broken/clashed sets: 118 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220285 /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `1' /scratch/stefan/7769890/working/building/REAL300000220285/1 /scratch/stefan/7769890/working/building/REAL300000220285 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/287 `/scratch/stefan/7769890/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CC[NH+](C)CC3)C(F)=C2)=N1) `REAL300000220285.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220285/1/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: REAL300000220285 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CC[NH+](C)CC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 9, 6, 5, 5, 5, 1, 15, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 36, 36, 36, 59, 83, 83, 36, 36, 36, 6, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 36, 36, 36, 36, 59, 59, 36, 6, 6, 1, 1, 8, 8, 8, 8, 8, 8, 7, 8, 8, 8, 8, 1] 100 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 50, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 290 number of broken/clashed sets: 100 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220285 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CC[NH+](C)CC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 9, 6, 5, 5, 5, 1, 15, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 36, 36, 36, 36, 73, 73, 73, 73, 73, 73, 73, 36, 36, 36, 1, 2, 2, 2, 3, 3, 1, 11, 11, 36, 36, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 36] 100 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220285 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CC[NH+](C)CC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 9, 6, 5, 5, 5, 1, 15, 1, 8, 7, 7, 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, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [73, 73, 73, 73, 100, 100, 100, 73, 73, 73, 24, 24, 7, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 73, 73, 73, 73, 100, 100, 73, 24, 24, 8, 8, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 8] 100 rigid atoms, others: [48, 49, 39, 40, 41, 42, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 50]) total number of confs: 295 number of broken/clashed sets: 100 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220285 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220285 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 1: /scratch/stefan/7769890/working/building/REAL300000220285/1.* 0: /scratch/stefan/7769890/working/building/REAL300000220285/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220285 Building REAL300000220286 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220286' /scratch/stefan/7769890/working/building/REAL300000220286 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220286 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220286/0 /scratch/stefan/7769890/working/building/REAL300000220286 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/288 `/scratch/stefan/7769890/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3F)=C2)=N1) `REAL300000220286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220286 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 44, 73, 73, 23, 23, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 2, 9, 9, 9, 1, 23, 23, 23, 23, 44, 44, 23, 5, 5, 1, 1, 1, 2, 2, 9, 9, 8, 9, 1] 201 rigid atoms, others: [37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45]) total number of confs: 305 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220286 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 8, 8, 23, 23, 23, 23, 23, 39, 39, 121, 121, 53, 121, 121, 121, 23, 1, 2, 2, 2, 3, 3, 1, 8, 8, 23, 23, 23, 39, 39, 121, 121, 121, 121, 23] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 432 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220286 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=CC=C3F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 121, 121, 201, 201, 201, 121, 121, 121, 33, 33, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 121, 121, 121, 121, 201, 201, 121, 33, 33, 9, 8, 9, 6, 6, 1, 1, 1, 1, 9] 201 rigid atoms, others: [42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46]) total number of confs: 689 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220286 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220286 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220286/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220286 Building REAL300000220287 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220287' /scratch/stefan/7769890/working/building/REAL300000220287 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220287 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220287/0 /scratch/stefan/7769890/working/building/REAL300000220287 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/289 `/scratch/stefan/7769890/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)=CC1=CC=CC=C1) `REAL300000220287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220287 none CC(C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)=CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 9, 9, 24, 24, 24, 24, 24, 41, 41, 41, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 41, 41, 24, 24, 24, 24, 4, 1, 1, 1, 1, 1] 41 rigid atoms, others: [35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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: REAL300000220287 none CC(C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)=CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 23, 23, 24, 24, 23, 24, 24, 24, 24, 24, 10, 10, 3, 3, 2, 2, 2, 1, 24, 24, 24, 24, 24, 24] 41 rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220287 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220287 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220287/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220287 Building REAL300000220288 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220288' /scratch/stefan/7769890/working/building/REAL300000220288 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220288 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220288/0 /scratch/stefan/7769890/working/building/REAL300000220288 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/290 `/scratch/stefan/7769890/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CS2)C=C1) `REAL300000220288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220288 none CC1=CC=C(C2=NC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 14, 1, 1, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [2, 1, 3, 3, 1, 1, 1, 1, 1, 12, 12, 42, 42, 43, 43, 43, 63, 63, 63, 43, 43, 43, 1, 1, 3, 3, 4, 4, 4, 4, 4, 12, 12, 63, 63, 43, 43, 43, 43, 1, 4, 4] 63 rigid atoms, others: [4, 5, 6, 7, 8, 39, 22, 23] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) 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: REAL300000220288 none CC1=CC=C(C2=NC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 14, 1, 1, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [1, 1, 1, 1, 1, 1, 4, 4, 5, 30, 30, 53, 53, 53, 53, 53, 63, 63, 63, 53, 53, 53, 4, 4, 1, 1, 2, 2, 2, 1, 1, 30, 30, 63, 63, 53, 53, 53, 53, 4, 1, 1] 63 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 41, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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: REAL300000220288 none CC1=CC=C(C2=NC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 14, 1, 1, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [52, 43, 52, 52, 43, 43, 43, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 43, 43, 52, 52, 52, 52, 52, 52, 52, 11, 11, 3, 3, 2, 2, 2, 1, 43, 52, 52] 63 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 150 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220288 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220288 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220288/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220288 Building REAL300000220289 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220289' /scratch/stefan/7769890/working/building/REAL300000220289 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220289 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220289/0 /scratch/stefan/7769890/working/building/REAL300000220289 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/291 `/scratch/stefan/7769890/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC3=CC=CC=C3O2)N1) `REAL300000220289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220289 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC3=CC=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 97, 112, 112, 58, 58, 58, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 58, 59, 59, 59, 97, 97, 9, 9, 1, 2, 2, 2, 13, 13, 13, 13, 13, 58] 201 rigid atoms, others: [36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 393 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220289 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC3=CC=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 58, 58, 58, 58, 58, 58, 155, 155, 155, 155, 155, 155, 155, 155, 1, 2, 2, 2, 3, 3, 10, 10, 58, 59, 59, 59, 155, 155, 155, 155, 155, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 45, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 244 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220289 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC3=CC=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 201, 201, 201, 155, 155, 155, 62, 62, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 201, 201, 62, 62, 13, 13, 13, 13, 1, 1, 1, 1, 1, 155] 201 rigid atoms, others: [40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45]) total number of confs: 544 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220289 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220289 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220289/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220289 Building REAL300000220290 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220290' /scratch/stefan/7769890/working/building/REAL300000220290 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220290 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220290/0 /scratch/stefan/7769890/working/building/REAL300000220290 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/292 `/scratch/stefan/7769890/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=NC=C2)N1) `REAL300000220290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220290 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=NC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 126, 148, 148, 84, 84, 84, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 84, 84, 84, 84, 126, 126, 11, 11, 1, 2, 2, 2, 7, 7, 7, 7, 84] 156 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 468 number of broken/clashed sets: 155 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220290 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=NC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 84, 84, 84, 84, 84, 84, 140, 140, 84, 140, 140, 1, 2, 2, 2, 3, 3, 11, 11, 84, 84, 84, 84, 140, 140, 140, 140, 1] 156 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 41, 25] set([4, 5, 6, 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, 39, 40]) total number of confs: 357 number of broken/clashed sets: 155 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220290 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=NC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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: [140, 140, 140, 140, 156, 156, 156, 140, 140, 140, 43, 43, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 156, 156, 43, 43, 7, 7, 7, 7, 1, 1, 1, 1, 140] 156 rigid atoms, others: [37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 317 number of broken/clashed sets: 155 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220290 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220290 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220290/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220290 Building REAL300000220291 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220291' /scratch/stefan/7769890/working/building/REAL300000220291 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220291 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220291/0 /scratch/stefan/7769890/working/building/REAL300000220291 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/293 `/scratch/stefan/7769890/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C([N+](=O)[O-])C=C2)N1) `REAL300000220291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220291 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C([N+](=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 123, 131, 131, 73, 73, 73, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 7, 7, 73, 73, 73, 73, 123, 123, 12, 12, 1, 2, 2, 2, 7, 7, 7, 7, 73] 163 rigid atoms, others: [36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 455 number of broken/clashed sets: 162 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220291 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C([N+](=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 73, 73, 73, 73, 73, 73, 114, 114, 106, 114, 114, 114, 114, 114, 1, 2, 2, 2, 3, 3, 11, 11, 73, 73, 73, 73, 114, 114, 114, 114, 1] 163 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 44, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 234 number of broken/clashed sets: 162 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220291 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C([N+](=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 163, 163, 163, 114, 114, 114, 41, 41, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 114, 114, 114, 114, 163, 163, 41, 41, 7, 7, 7, 7, 1, 1, 1, 1, 114] 163 rigid atoms, others: [40, 41, 42, 43, 18, 19, 20, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44]) total number of confs: 490 number of broken/clashed sets: 162 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220291 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220291 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220291/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220291 Building REAL300000220292 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220292' /scratch/stefan/7769890/working/building/REAL300000220292 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220292 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220292/0 /scratch/stefan/7769890/working/building/REAL300000220292 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/294 `/scratch/stefan/7769890/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(C)(=O)=O)C=C2)=N1) `REAL300000220292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220292 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(C)(=O)=O)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 21, 21, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 11, 11, 11, 11, 17, 17, 11, 4, 4, 1, 1, 3, 3, 3, 1, 1] 31 rigid atoms, others: [32, 33, 37, 38, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 80 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: REAL300000220292 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(C)(=O)=O)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 7, 7, 11, 11, 7, 7, 21, 21, 21, 11, 11, 1, 2, 2, 2, 3, 3, 1, 7, 7, 11, 11, 21, 21, 21, 11, 11] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 118 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220292 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220292 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220292/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220292 Building REAL300000220293 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220293' /scratch/stefan/7769890/working/building/REAL300000220293 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220293 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220293/0 /scratch/stefan/7769890/working/building/REAL300000220293 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/295 `/scratch/stefan/7769890/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=C2COC3=CC=C(F)C=C23)N1) `REAL300000220293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220293 none CC1=C(CC(=O)[O-])C(=O)N=C(C=C2COC3=CC=C(F)C=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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, 9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 1, 1, 1, 1, 1, 1, 5] 9 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 22, 23, 24, 25, 26, 27]) total number of confs: 30 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: REAL300000220293 none CC1=C(CC(=O)[O-])C(=O)N=C(C=C2COC3=CC=C(F)C=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 3, 3, 5, 5, 5, 5, 5, 5, 1] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 26 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220293 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220293 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220293/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220293 Building REAL300000220294 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220294' /scratch/stefan/7769890/working/building/REAL300000220294 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220294 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220294/0 /scratch/stefan/7769890/working/building/REAL300000220294 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/296 `/scratch/stefan/7769890/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C(C)(C)C)N1) `REAL300000220294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220294 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C(C)(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 35, 35, 35, 48, 48, 48, 35, 35, 35, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 35, 36, 36, 36, 48, 48, 7, 7, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35] 52 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 157 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220294 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C(C)(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 35, 35, 35, 35, 35, 38, 38, 38, 1, 2, 2, 2, 3, 3, 12, 12, 35, 35, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1] 52 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 41] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 122 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220294 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220294 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220294/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220294 Building REAL300000220295 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220295' /scratch/stefan/7769890/working/building/REAL300000220295 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220295 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220295/0 /scratch/stefan/7769890/working/building/REAL300000220295 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/297 `/scratch/stefan/7769890/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2[N+](=O)[O-])OCCO3)=N1) `REAL300000220295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220295 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2[N+](=O)[O-])OCCO3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 5, 5, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 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: [31, 31, 31, 31, 37, 37, 37, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 31, 31, 31, 31, 37, 37, 31, 7, 7, 1, 1, 1, 1, 1, 1] 37 rigid atoms, others: [35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 83 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: REAL300000220295 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2[N+](=O)[O-])OCCO3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 5, 5, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 1, 11, 11, 31, 31, 31, 31, 31, 31] 37 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 77 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220295 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220295 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220295/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220295 Building REAL300000220296 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220296' /scratch/stefan/7769890/working/building/REAL300000220296 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220296 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220296/0 /scratch/stefan/7769890/working/building/REAL300000220296 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/298 `/scratch/stefan/7769890/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=CC=C3OCOC3=C2)N1) `REAL300000220296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220296 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=CC=C3OCOC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 100, 120, 120, 60, 61, 60, 12, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 10, 11, 11, 11, 11, 11, 61, 61, 61, 61, 100, 100, 12, 12, 1, 1, 11, 11, 11, 11, 11, 61] 201 rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 416 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220296 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=CC=C3OCOC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 61, 61, 61, 61, 61, 141, 141, 141, 141, 141, 141, 141, 141, 1, 2, 2, 2, 3, 3, 10, 10, 61, 61, 141, 141, 141, 141, 141, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 27, 42] set([4, 5, 6, 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, 41]) total number of confs: 226 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220296 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=CC=C3OCOC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 141, 201, 201, 201, 141, 141, 141, 56, 56, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 201, 201, 56, 56, 11, 11, 1, 1, 1, 1, 1, 141] 201 rigid atoms, others: [37, 38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 604 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220296 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220296 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220296/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220296 Building REAL300000220297 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220297' /scratch/stefan/7769890/working/building/REAL300000220297 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220297 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220297/0 /scratch/stefan/7769890/working/building/REAL300000220297 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/299 `/scratch/stefan/7769890/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OC2CCCC2)=N1) `REAL300000220297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220297 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OC2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 93, 127, 127, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 50, 50, 50, 50, 93, 93, 50, 8, 8, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 486 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220297 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OC2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 50, 50, 31, 50, 50, 50, 101, 115, 115, 115, 115, 1, 2, 2, 2, 3, 3, 1, 11, 11, 50, 50, 50, 50, 115, 115, 115, 115, 115, 115, 115, 115, 115] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 306 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220297 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OC2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 115, 201, 201, 201, 115, 115, 115, 37, 37, 12, 12, 12, 9, 12, 12, 6, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 201, 201, 115, 37, 37, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 724 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220297 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220297 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220297/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220297 Building REAL300000220298 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220298' /scratch/stefan/7769890/working/building/REAL300000220298 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220298 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220298/0 /scratch/stefan/7769890/working/building/REAL300000220298 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/300 `/scratch/stefan/7769890/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CSC=C3)=N2)=N1) `REAL300000220298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220298 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CSC=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 14, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 52, 52, 52, 74, 75, 75, 52, 52, 52, 12, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 52, 53, 53, 53, 74, 74, 51, 13, 12, 1, 5, 5, 5] 110 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 224 number of broken/clashed sets: 109 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220298 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CSC=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 14, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 52, 52, 52, 52, 92, 92, 92, 92, 52, 1, 2, 2, 2, 3, 3, 1, 12, 12, 52, 92, 92, 92] 110 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 173 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220298 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CSC=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 14, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [92, 92, 92, 92, 110, 110, 110, 92, 92, 92, 31, 31, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 92, 92, 92, 92, 110, 110, 91, 31, 31, 5, 1, 1, 1] 110 rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 255 number of broken/clashed sets: 109 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220298 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220298 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220298/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220298 Building REAL300000220299 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220299' /scratch/stefan/7769890/working/building/REAL300000220299 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220299 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220299/0 /scratch/stefan/7769890/working/building/REAL300000220299 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/301 `/scratch/stefan/7769890/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC([N+](=O)[O-])=CC=C2OC(F)F)=N1) `REAL300000220299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220299 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC([N+](=O)[O-])=CC=C2OC(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 85, 143, 143, 56, 56, 56, 9, 9, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 40, 40, 56, 56, 56, 56, 85, 85, 56, 9, 9, 1, 1, 1, 40] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 606 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220299 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC([N+](=O)[O-])=CC=C2OC(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 56, 56, 56, 56, 56, 23, 56, 56, 56, 130, 182, 182, 1, 2, 2, 2, 3, 3, 1, 11, 11, 56, 56, 56, 182] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 635 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220299 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220299 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220299/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220299 Building REAL300000220300 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220300' /scratch/stefan/7769890/working/building/REAL300000220300 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220300 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220300/0 /scratch/stefan/7769890/working/building/REAL300000220300 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/302 `/scratch/stefan/7769890/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)S2)C=C1) `REAL300000220300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220300 none CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 7, 7, 1, 1, 1, 1, 1, 1, 11, 11, 45, 45, 45, 45, 45, 55, 56, 56, 45, 45, 45, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 11, 11, 55, 55, 45, 45, 45, 45, 7, 7] 91 rigid atoms, others: [4, 5, 6, 7, 8, 9, 32, 23, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) 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: REAL300000220300 none CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 1, 7, 7, 7, 7, 41, 41, 79, 79, 79, 79, 79, 91, 91, 91, 79, 79, 79, 7, 1, 1, 2, 2, 2, 1, 1, 7, 7, 41, 41, 91, 91, 79, 79, 79, 79, 1, 1] 91 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 42, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220300 none CC1=CC=C(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [76, 76, 79, 79, 45, 45, 45, 45, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 45, 79, 79, 79, 79, 79, 79, 79, 45, 45, 11, 11, 3, 3, 2, 2, 2, 1, 79, 79] 91 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 181 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220300 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220300 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220300/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220300 Building REAL300000220301 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220301' /scratch/stefan/7769890/working/building/REAL300000220301 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220301 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220301/0 /scratch/stefan/7769890/working/building/REAL300000220301 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/303 `/scratch/stefan/7769890/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1) `REAL300000220301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220301 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 67, 104, 67, 67, 67, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 67, 104, 104, 104, 68, 68, 12, 12, 2, 2, 2, 3, 3, 1] 124 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 261 number of broken/clashed sets: 123 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220301 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 67, 67, 97, 101, 101, 67, 68, 67, 1, 13, 13, 13, 1, 1, 12, 12, 68, 68, 68, 97, 97, 67] 124 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 318 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220301 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220301 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220301/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220301 Building REAL300000220302 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220302' /scratch/stefan/7769890/working/building/REAL300000220302 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220302 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220302/0 /scratch/stefan/7769890/working/building/REAL300000220302 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/304 `/scratch/stefan/7769890/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CO2)=N1) `REAL300000220302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220302 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CO2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 33, 33, 33, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 33, 33, 27, 10, 9, 1, 1] 33 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 82 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: REAL300000220302 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CO2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 1, 9, 9, 27, 27] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 66 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220302 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220302 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220302/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220302 Building REAL300000220303 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220303' /scratch/stefan/7769890/working/building/REAL300000220303 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220303 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220303/0 /scratch/stefan/7769890/working/building/REAL300000220303 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/305 `/scratch/stefan/7769890/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN3C=C(Cl)C=CC3=N2)N1) `REAL300000220303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220303 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN3C=C(Cl)C=CC3=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 16, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 19, 19, 19, 29, 29, 29, 18, 19, 18, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 29, 29, 11, 11, 1, 1, 1, 1, 19] 29 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 100 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: REAL300000220303 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN3C=C(Cl)C=CC3=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 16, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 11, 11, 19, 19, 19, 19, 1] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 59 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220303 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220303 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220303/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220303 Building REAL300000220304 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220304' /scratch/stefan/7769890/working/building/REAL300000220304 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220304 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220304/0 /scratch/stefan/7769890/working/building/REAL300000220304 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/306 `/scratch/stefan/7769890/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C3OC(C)(C)CCC3=C2)=N1) `REAL300000220304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220304 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C3OC(C)(C)CCC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 32, 32, 32, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 32, 32, 18, 6, 6, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1] 32 rigid atoms, others: [34, 35, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 127 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: REAL300000220304 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C3OC(C)(C)CCC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 3, 1, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 59 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220304 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220304 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220304/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220304 Building REAL300000220305 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220305' /scratch/stefan/7769890/working/building/REAL300000220305 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220305 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220305/0 /scratch/stefan/7769890/working/building/REAL300000220305 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/307 `/scratch/stefan/7769890/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(C)C(=O)[O-])=C2)=N1) `REAL300000220305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220305 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(C)C(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 50, 83, 83, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 23, 23, 1, 29, 29, 29, 29, 50, 50, 29, 5, 5, 1, 1, 1, 15, 15, 15, 15, 1] 201 rigid atoms, others: [34, 35, 36, 41, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 368 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220305 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(C)C(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 29, 29, 76, 128, 128, 167, 167, 29, 1, 2, 2, 2, 3, 3, 1, 9, 9, 29, 29, 29, 128, 128, 128, 128, 29] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 552 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220305 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220305 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220305/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220305 Building REAL300000220306 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220306' /scratch/stefan/7769890/working/building/REAL300000220306 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220306 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220306/0 /scratch/stefan/7769890/working/building/REAL300000220306 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/308 `/scratch/stefan/7769890/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCCCC#N) `REAL300000220306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220306 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCCCC#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 55, 60, 107, 123, 123, 38, 38, 38, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 60, 60, 107, 107, 123, 123] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 542 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220306 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCCCC#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 35, 54, 54, 21, 21, 21, 1, 1, 1, 5, 9, 15, 17, 17, 3, 3, 3, 1, 1, 5, 5, 21, 21, 21, 35, 35, 21, 1, 9, 9, 15, 15, 17, 17] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 41, 20, 21, 22, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 259 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220306 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220306 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220306/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220306 Building REAL300000220307 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220307' /scratch/stefan/7769890/working/building/REAL300000220307 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220307 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220307/0 /scratch/stefan/7769890/working/building/REAL300000220307 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/309 `/scratch/stefan/7769890/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(F)(F)F)C=C2)=N1) `REAL300000220307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220307 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 42, 64, 64, 26, 26, 26, 4, 4, 1, 1, 1, 1, 1, 1, 7, 26, 26, 26, 26, 1, 1, 26, 26, 26, 26, 42, 42, 26, 4, 4, 1, 1, 26, 26, 1, 1] 201 rigid atoms, others: [34, 35, 38, 39, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 288 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220307 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 13, 13, 26, 26, 13, 13, 71, 145, 145, 145, 145, 26, 26, 1, 2, 2, 2, 3, 3, 1, 13, 13, 26, 26, 145, 145, 26, 26] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 516 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220307 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220307 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220307/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220307 Building REAL300000220308 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220308' /scratch/stefan/7769890/working/building/REAL300000220308 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220308 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220308/0 /scratch/stefan/7769890/working/building/REAL300000220308 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/310 `/scratch/stefan/7769890/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC) `REAL300000220308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220308 none CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 64, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 62, 97, 145, 145, 145, 145, 145, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 97, 97, 97, 97, 97] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 40, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 730 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220308 none CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 5, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 40, 64, 64, 21, 21, 21, 1, 1, 1, 7, 15, 22, 22, 22, 22, 22, 1, 1, 5, 5, 21, 21, 21, 40, 40, 21, 1, 15, 15, 16, 16, 16] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 41, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 358 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220308 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220308 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220308/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220308 Building REAL300000220309 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220309' /scratch/stefan/7769890/working/building/REAL300000220309 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220309 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220309/0 /scratch/stefan/7769890/working/building/REAL300000220309 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/311 `/scratch/stefan/7769890/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)COC1=C(C)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C) `REAL300000220309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220309 none COC(=O)COC1=C(C)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 88, 151, 29, 26, 19, 29, 29, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 29, 29, 29, 151, 151, 151, 88, 88, 29, 29, 29, 29, 10, 10, 2, 2, 2, 3, 3, 1, 29, 29, 29, 29] 201 rigid atoms, others: [44, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 598 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220309 none COC(=O)COC1=C(C)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 5, 26, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 57, 97, 97, 29, 29, 29, 1, 1, 1, 27, 27, 27, 5, 5, 2, 2, 2, 1, 5, 5, 29, 29, 29, 57, 57, 29, 1, 2, 2, 2] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 45, 25, 36, 26, 27] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 442 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220309 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220309 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220309/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220309 Building REAL300000220310 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220310' /scratch/stefan/7769890/working/building/REAL300000220310 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220310 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220310/0 /scratch/stefan/7769890/working/building/REAL300000220310 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/312 `/scratch/stefan/7769890/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220310 none COCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 113, 63, 63, 21, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 140, 140, 140, 140, 140, 113, 113, 63, 63, 21, 21, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21] 201 rigid atoms, others: [45, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46]) total number of confs: 484 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220310 none COCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 40, 48, 48, 21, 21, 21, 1, 15, 15, 15, 14, 14, 10, 10, 6, 6, 1, 1, 1, 5, 5, 21, 21, 21, 40, 40, 21, 1] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 46, 25, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220310 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220310 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220310/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220310 Building REAL300000220311 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220311' /scratch/stefan/7769890/working/building/REAL300000220311 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220311 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220311/0 /scratch/stefan/7769890/working/building/REAL300000220311 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/313 `/scratch/stefan/7769890/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1SC) `REAL300000220311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220311 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'S.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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 46, 46, 46, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 46, 46, 46, 46, 154, 95, 95, 95, 46, 12, 12, 3, 3, 2, 2, 2, 1, 46, 46, 154, 154, 154] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 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: 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: REAL300000220311 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1SC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'S.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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 46, 46, 46, 46, 46, 77, 127, 127, 46, 46, 46, 1, 1, 1, 1, 9, 4, 4, 4, 1, 6, 6, 77, 77, 46, 46, 46, 46, 1, 1, 10, 10, 10] 201 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 36, 27, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 459 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220311 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220311 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220311/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220311 Building REAL300000220312 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220312' /scratch/stefan/7769890/working/building/REAL300000220312 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220312 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220312/0 /scratch/stefan/7769890/working/building/REAL300000220312 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/314 `/scratch/stefan/7769890/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC(C)C)=C2)N1) `REAL300000220312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220312 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC(C)C)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 67, 100, 100, 36, 36, 36, 5, 5, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 1, 36, 36, 36, 36, 67, 67, 5, 5, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 1, 36] 201 rigid atoms, others: [32, 33, 41, 12, 13, 14, 15, 16, 17, 18, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 421 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220312 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC(C)C)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 36, 36, 36, 36, 36, 123, 148, 148, 36, 1, 2, 2, 2, 3, 3, 10, 10, 36, 36, 36, 148, 148, 148, 148, 148, 148, 148, 36, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 42] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 345 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220312 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220312 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220312/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220312 Building REAL300000220313 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220313' /scratch/stefan/7769890/working/building/REAL300000220313 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220313 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220313/0 /scratch/stefan/7769890/working/building/REAL300000220313 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/315 `/scratch/stefan/7769890/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCCC(=O)[O-])=C2)=N1) `REAL300000220313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220313 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCCC(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 55, 87, 87, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 7, 9, 15, 15, 1, 29, 29, 29, 29, 55, 55, 29, 5, 5, 1, 1, 1, 7, 7, 9, 9, 1] 201 rigid atoms, others: [34, 35, 36, 41, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 374 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220313 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCCC(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 29, 29, 120, 122, 128, 156, 156, 29, 1, 2, 2, 2, 3, 3, 1, 9, 9, 29, 29, 29, 122, 122, 128, 128, 29] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 351 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220313 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220313 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220313/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220313 Building REAL300000220314 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220314' /scratch/stefan/7769890/working/building/REAL300000220314 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220314 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220314/0 /scratch/stefan/7769890/working/building/REAL300000220314 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/316 `/scratch/stefan/7769890/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC(F)=CC(F)=C3)C=C2)=N1) `REAL300000220314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220314 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC(F)=CC(F)=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 30, 45, 45, 19, 19, 19, 4, 4, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 11, 19, 19, 19, 1, 1, 19, 19, 19, 19, 30, 30, 19, 4, 4, 1, 1, 19, 11, 19, 1, 1] 201 rigid atoms, others: [37, 38, 42, 43, 12, 13, 14, 15, 16, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 193 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220314 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC(F)=CC(F)=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 19, 19, 12, 18, 86, 139, 139, 139, 102, 139, 139, 139, 19, 19, 1, 2, 2, 2, 3, 3, 1, 12, 12, 19, 19, 139, 103, 139, 19, 19] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 354 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220314 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC(F)=CC(F)=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 153, 201, 201, 201, 153, 153, 153, 51, 51, 8, 8, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 153, 153, 153, 153, 201, 201, 153, 51, 51, 26, 26, 1, 1, 1, 26, 26] 201 rigid atoms, others: [39, 40, 41, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43]) total number of confs: 592 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220314 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220314 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220314/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220314 Building REAL300000220315 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220315' /scratch/stefan/7769890/working/building/REAL300000220315 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220315 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220315/0 /scratch/stefan/7769890/working/building/REAL300000220315 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/317 `/scratch/stefan/7769890/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(F)=C2)=N1) `REAL300000220315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220315 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 20, 20, 20, 29, 29, 29, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 29, 29, 20, 7, 7, 1, 1, 1] 29 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 87 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220315 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 1, 9, 9, 20, 20, 20] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 61 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220315 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220315 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220315/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220315 Building REAL300000220316 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220316' /scratch/stefan/7769890/working/building/REAL300000220316 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220316 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220316/0 /scratch/stefan/7769890/working/building/REAL300000220316 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/318 `/scratch/stefan/7769890/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Cl)C=C(Cl)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220316 none COC1=C(Cl)C=C(Cl)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [70, 60, 60, 60, 60, 28, 60, 60, 60, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 70, 70, 70, 60, 60, 12, 12, 2, 2, 2, 3, 3, 1] 96 rigid atoms, others: [36, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 235 number of broken/clashed sets: 96 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220316 none COC1=C(Cl)C=C(Cl)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 60, 60, 60, 60, 60, 87, 96, 96, 60, 60, 60, 7, 7, 7, 1, 1, 11, 11, 60, 60, 60, 87, 87, 60] 96 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 287 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220316 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220316 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220316/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220316 Building REAL300000220317 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220317' /scratch/stefan/7769890/working/building/REAL300000220317 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220317 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220317/0 /scratch/stefan/7769890/working/building/REAL300000220317 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/319 `/scratch/stefan/7769890/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC) `REAL300000220317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220317 none CCOCC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 100, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 27, 27, 19, 26, 65, 125, 125, 125, 125, 125, 100, 100, 27, 9, 9, 2, 2, 2, 3, 3, 1, 27, 27, 65, 65, 65] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 508 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220317 none CCOCC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 5, 1, 1, 1, 1, 1, 5, 5, 27, 27, 27, 27, 27, 46, 69, 69, 27, 27, 27, 1, 1, 1, 1, 3, 11, 11, 11, 10, 10, 5, 5, 1, 5, 5, 27, 27, 27, 46, 46, 27, 1, 1, 4, 4, 4] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 42, 43, 21, 22, 23, 24] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46]) total number of confs: 278 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220317 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220317 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220317/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220317 Building REAL300000220318 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220318' /scratch/stefan/7769890/working/building/REAL300000220318 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220318 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220318/0 /scratch/stefan/7769890/working/building/REAL300000220318 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/320 `/scratch/stefan/7769890/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([N+](=O)[O-])C([O-])=C2)N1) `REAL300000220318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220318 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([N+](=O)[O-])C([O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 4, 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: [25, 25, 25, 25, 28, 28, 28, 25, 25, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 28, 28, 7, 7, 1, 1, 1, 25] 28 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 56 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: REAL300000220318 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([N+](=O)[O-])C([O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 10, 10, 25, 25, 25, 1] 28 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 71 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220318 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220318 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220318/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220318 Building REAL300000220319 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220319' /scratch/stefan/7769890/working/building/REAL300000220319 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220319 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220319/0 /scratch/stefan/7769890/working/building/REAL300000220319 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/321 `/scratch/stefan/7769890/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=NC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C12) `REAL300000220319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220319 none CC1=NN(C)C2=NC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 3, 3, 2, 2, 2, 1, 16] 29 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) 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: REAL300000220319 none CC1=NN(C)C2=NC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 16, 29, 29, 29, 16, 16, 16, 1, 1, 2, 2, 2, 2, 2, 2, 1, 5, 5, 29, 29, 16, 16, 16, 16, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 40, 23, 24, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220319 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220319 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220319/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220319 Building REAL300000220320 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220320' /scratch/stefan/7769890/working/building/REAL300000220320 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220320 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220320/0 /scratch/stefan/7769890/working/building/REAL300000220320 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/322 `/scratch/stefan/7769890/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)C2=CC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CN=C2S1) `REAL300000220320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220320 none COC(=O)C1=C(C)C2=CC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CN=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 41, 101, 41, 41, 41, 41, 41, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 41, 41, 41, 41, 101, 101, 101, 41, 41, 41, 41, 12, 12, 2, 2, 2, 3, 3, 1, 41] 131 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43]) total number of confs: 277 number of broken/clashed sets: 131 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220320 none COC(=O)C1=C(C)C2=CC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CN=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 41, 41, 72, 94, 94, 41, 41, 41, 1, 1, 1, 1, 13, 13, 13, 2, 2, 2, 1, 7, 7, 41, 41, 41, 72, 72, 41, 1] 131 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 43, 34, 24, 25, 26, 27] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 361 number of broken/clashed sets: 131 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220320 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220320 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220320/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220320 Building REAL300000220321 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220321' /scratch/stefan/7769890/working/building/REAL300000220321 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220321 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220321/0 /scratch/stefan/7769890/working/building/REAL300000220321 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/323 `/scratch/stefan/7769890/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC) `REAL300000220321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220321 none C=C(C)COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 121, 137, 96, 27, 27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 27, 27, 27, 27, 51, 137, 137, 137, 137, 137, 121, 121, 27, 8, 8, 2, 2, 2, 3, 3, 1, 27, 27, 51, 51, 51] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 422 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220321 none C=C(C)COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 20, 25, 7, 1, 1, 1, 1, 1, 5, 5, 27, 27, 27, 27, 27, 49, 82, 82, 27, 27, 27, 1, 1, 1, 1, 3, 25, 25, 25, 25, 25, 20, 20, 1, 5, 5, 27, 27, 27, 49, 49, 27, 1, 1, 3, 3, 3] 201 rigid atoms, others: [34, 4, 5, 6, 7, 8, 43, 44, 22, 23, 24, 25] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 388 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220321 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220321 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220321/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220321 Building REAL300000220322 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220322' /scratch/stefan/7769890/working/building/REAL300000220322 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220322 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220322/0 /scratch/stefan/7769890/working/building/REAL300000220322 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/324 `/scratch/stefan/7769890/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220322 none CCCCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 60, 60, 21, 21, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 60, 60, 21, 21, 21, 6, 6, 2, 2, 2, 3, 3, 1, 21] 201 rigid atoms, others: [50, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51]) total number of confs: 440 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220322 none CCCCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 34, 44, 44, 21, 21, 21, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 1, 1, 1, 5, 5, 21, 21, 21, 34, 34, 21, 1] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 40, 51, 41, 26, 42] set([0, 1, 2, 3, 4, 5, 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, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 191 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220322 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220322 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220322/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220322 Building REAL300000220323 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220323' /scratch/stefan/7769890/working/building/REAL300000220323 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220323 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220323/0 /scratch/stefan/7769890/working/building/REAL300000220323 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/325 `/scratch/stefan/7769890/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1O) `REAL300000220323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220323 none C=CCC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 3, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [97, 63, 29, 29, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 29, 29, 29, 62, 29, 29, 97, 97, 97, 63, 63, 29, 10, 10, 3, 3, 1, 1, 1, 1, 29, 62, 62, 62, 58] 402 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44]) total number of confs: 471 number of broken/clashed sets: 203 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220323 none C=CCC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 3, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 54, 93, 93, 29, 29, 29, 1, 1, 1, 3, 1, 1, 11, 11, 11, 5, 5, 1, 5, 5, 54, 54, 29, 29, 29, 29, 1, 3, 3, 3, 2] 402 rigid atoms, others: [2, 3, 4, 5, 6, 40, 20, 21, 22, 24, 25, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 379 number of broken/clashed sets: 203 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220323 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220323 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220323/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220323 Building REAL300000220324 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220324' /scratch/stefan/7769890/working/building/REAL300000220324 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220324 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220324/0 /scratch/stefan/7769890/working/building/REAL300000220324 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/326 `/scratch/stefan/7769890/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(F)F)=C2)=N1) `REAL300000220324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220324 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 51, 68, 68, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 10, 16, 16, 1, 29, 29, 29, 29, 51, 51, 29, 5, 5, 1, 1, 1, 16, 1] 201 rigid atoms, others: [32, 33, 34, 36, 12, 13, 14, 15, 16, 17, 18, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 279 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220324 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 29, 29, 98, 128, 128, 29, 1, 2, 2, 2, 3, 3, 1, 9, 9, 29, 29, 29, 128, 29] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 346 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220324 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220324 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220324/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220324 Building REAL300000220325 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220325' /scratch/stefan/7769890/working/building/REAL300000220325 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220325 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220325/0 /scratch/stefan/7769890/working/building/REAL300000220325 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/327 `/scratch/stefan/7769890/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC) `REAL300000220325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220325 none CCCCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 90, 85, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 19, 19, 19, 19, 34, 139, 139, 139, 139, 139, 139, 139, 139, 139, 90, 90, 19, 5, 5, 2, 2, 2, 3, 3, 1, 19, 19, 34, 34, 34] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52]) total number of confs: 447 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220325 none CCCCCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 9, 7, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 19, 32, 35, 35, 19, 19, 19, 1, 1, 1, 1, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 1, 5, 5, 19, 19, 19, 32, 32, 19, 1, 1, 3, 3, 3] 201 rigid atoms, others: [5, 6, 39, 8, 9, 7, 48, 49, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220325 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220325 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220325/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220325 Building REAL300000220326 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220326' /scratch/stefan/7769890/working/building/REAL300000220326 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220326 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220326/0 /scratch/stefan/7769890/working/building/REAL300000220326 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/328 `/scratch/stefan/7769890/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3OC2)N1) `REAL300000220326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220326 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3OC2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 25, 25, 3, 3, 1, 1, 1, 1, 1, 1, 1, 13] 25 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 95 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: REAL300000220326 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3OC2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 3, 3, 5, 5, 13, 13, 13, 13, 13, 13, 13, 1] 25 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 47 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220326 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220326 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220326/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220326 Building REAL300000220327 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220327' /scratch/stefan/7769890/working/building/REAL300000220327 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220327 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220327/0 /scratch/stefan/7769890/working/building/REAL300000220327 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/329 `/scratch/stefan/7769890/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=CC(Cl)=CC(Cl)=C3OC2)=N1) `REAL300000220327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220327 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=CC(Cl)=CC(Cl)=C3OC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 29, 29, 29, 21, 21, 21, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 29, 29, 21, 3, 3, 1, 1, 1, 1, 1] 29 rigid atoms, others: [34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 32, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 76 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220327 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=CC(Cl)=CC(Cl)=C3OC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 10, 10, 21, 21, 21, 21, 21] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220327 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220327 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220327/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220327 Building REAL300000220328 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220328' /scratch/stefan/7769890/working/building/REAL300000220328 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220328 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220328/0 /scratch/stefan/7769890/working/building/REAL300000220328 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/330 `/scratch/stefan/7769890/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(Br)C=C1O) `REAL300000220328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220328 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(Br)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 4, 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: [65, 41, 41, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 41, 41, 41, 41, 41, 65, 65, 65, 41, 11, 11, 2, 2, 2, 3, 3, 1, 41, 82] 162 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 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: 162 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220328 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(Br)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 9, 9, 41, 41, 41, 41, 41, 63, 81, 81, 41, 41, 41, 1, 1, 1, 1, 1, 4, 4, 4, 1, 9, 9, 41, 41, 41, 63, 63, 41, 1, 2] 162 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 36, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 274 number of broken/clashed sets: 162 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220328 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220328 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220328/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220328 Building REAL300000220329 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220329' /scratch/stefan/7769890/working/building/REAL300000220329 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220329 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220329/0 /scratch/stefan/7769890/working/building/REAL300000220329 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/331 `/scratch/stefan/7769890/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C(Cl)=C2)N1) `REAL300000220329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220329 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 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: [22, 22, 22, 22, 27, 27, 27, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 27, 27, 6, 6, 1, 1, 2, 1, 22] 54 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 31, 33]) total number of confs: 66 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220329 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 22, 22, 20, 20, 22, 22, 22, 1, 2, 2, 2, 3, 3, 9, 9, 22, 22, 44, 22, 1] 54 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 114 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220329 /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `1' /scratch/stefan/7769890/working/building/REAL300000220329/1 /scratch/stefan/7769890/working/building/REAL300000220329 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 1 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/332 `/scratch/stefan/7769890/working/3D/332' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([O-])C(Cl)=C2)N1) `REAL300000220329.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220329/1/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: REAL300000220329 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([O-])C(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 19, 19, 19, 29, 29, 29, 19, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 29, 29, 7, 7, 1, 1, 1, 19] 29 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 92 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220329 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([O-])C(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 19, 19, 15, 17, 19, 19, 19, 1, 2, 2, 2, 3, 3, 9, 9, 19, 19, 19, 1] 29 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 76 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220329 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220329 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 1: /scratch/stefan/7769890/working/building/REAL300000220329/1.* 0: /scratch/stefan/7769890/working/building/REAL300000220329/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220329 Building REAL300000220330 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220330' /scratch/stefan/7769890/working/building/REAL300000220330 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220330 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220330/0 /scratch/stefan/7769890/working/building/REAL300000220330 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/333 `/scratch/stefan/7769890/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220330 none CCCCCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 131, 131, 131, 131, 60, 60, 20, 20, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 20, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 60, 60, 20, 20, 20, 6, 6, 2, 2, 2, 3, 3, 1, 20] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 53, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54]) total number of confs: 452 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220330 none CCCCCCCOC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 20, 20, 20, 20, 20, 33, 42, 42, 20, 20, 20, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 1, 1, 1, 5, 5, 20, 20, 20, 33, 33, 20, 1] 201 rigid atoms, others: [11, 7, 8, 9, 10, 43, 44, 45, 12, 13, 54, 27] set([0, 1, 2, 3, 4, 5, 6, 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, 41, 42, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220330 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220330 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220330/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220330 Building REAL300000220331 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220331' /scratch/stefan/7769890/working/building/REAL300000220331 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220331 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220331/0 /scratch/stefan/7769890/working/building/REAL300000220331 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/334 `/scratch/stefan/7769890/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCCC(C)C) `REAL300000220331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220331 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 20, 20, 20, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 20, 20, 20, 67, 71, 120, 120, 120, 38, 38, 38, 20, 20, 5, 5, 2, 2, 2, 3, 3, 1, 20, 71, 71, 120, 120, 120, 120, 120, 120, 120, 120, 120] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 474 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220331 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OCCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 20, 20, 20, 20, 20, 37, 57, 57, 20, 20, 20, 1, 1, 1, 5, 7, 12, 12, 12, 3, 3, 3, 1, 1, 5, 5, 20, 20, 20, 37, 37, 20, 1, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 41, 20, 21, 22, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 262 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220331 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220331 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220331/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220331 Building REAL300000220332 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220332' /scratch/stefan/7769890/working/building/REAL300000220332 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220332 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220332/0 /scratch/stefan/7769890/working/building/REAL300000220332 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/335 `/scratch/stefan/7769890/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(F)(F)F) `REAL300000220332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220332 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 29, 29, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 29, 29, 29, 29, 101, 141, 141, 141, 141, 67, 67, 67, 29, 9, 9, 2, 2, 2, 3, 3, 1, 29, 29, 141, 141] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 39] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 459 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220332 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 50, 82, 82, 29, 29, 29, 1, 1, 1, 1, 7, 18, 18, 18, 18, 3, 3, 3, 1, 5, 5, 29, 29, 29, 50, 50, 29, 1, 1, 18, 18] 201 rigid atoms, others: [1, 2, 3, 4, 5, 40, 41, 19, 20, 21, 22, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43]) total number of confs: 354 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220332 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220332 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220332/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220332 Building REAL300000220333 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220333' /scratch/stefan/7769890/working/building/REAL300000220333 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220333 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220333/0 /scratch/stefan/7769890/working/building/REAL300000220333 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/336 `/scratch/stefan/7769890/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC(F)=C3)S2)N1) `REAL300000220333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220333 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC(F)=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 64, 64, 97, 110, 110, 64, 64, 64, 11, 11, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 1, 65, 65, 65, 65, 97, 97, 11, 11, 1, 1, 12, 12, 12, 12, 65] 201 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 345 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220333 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC(F)=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 64, 64, 64, 64, 169, 169, 168, 169, 169, 169, 64, 1, 2, 2, 2, 3, 3, 11, 11, 65, 64, 169, 169, 169, 169, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 39] set([4, 5, 6, 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: 263 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220333 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC(F)=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 169, 201, 201, 201, 169, 169, 169, 85, 85, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 169, 169, 169, 169, 201, 201, 85, 85, 12, 12, 1, 1, 1, 1, 169] 201 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 512 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220333 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220333 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220333/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220333 Building REAL300000220334 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220334' /scratch/stefan/7769890/working/building/REAL300000220334 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220334 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220334/0 /scratch/stefan/7769890/working/building/REAL300000220334 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/337 `/scratch/stefan/7769890/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=C(OC)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220334 none CCOC1=C(OC)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 47, 12, 12, 25, 25, 66, 25, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 25, 25, 25, 65, 142, 142, 142, 142, 142, 66, 66, 66, 25, 12, 12, 2, 2, 2, 3, 3, 1, 25, 65, 65, 65] 201 rigid atoms, others: [43, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 701 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220334 none CCOC1=C(OC)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 2, 1, 1, 1, 1, 3, 1, 1, 1, 3, 3, 25, 25, 25, 25, 25, 47, 93, 93, 25, 25, 25, 1, 1, 1, 3, 15, 15, 15, 14, 14, 4, 4, 4, 1, 3, 3, 25, 25, 25, 47, 47, 25, 1, 4, 4, 4] 201 rigid atoms, others: [2, 3, 4, 5, 7, 8, 9, 44, 35, 23, 24, 25] set([0, 1, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 393 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220334 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220334 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220334/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220334 Building REAL300000220335 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220335' /scratch/stefan/7769890/working/building/REAL300000220335 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220335 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220335/0 /scratch/stefan/7769890/working/building/REAL300000220335 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/338 `/scratch/stefan/7769890/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220335 none CC1=CC(F)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [21, 21, 21, 19, 21, 21, 21, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 21, 21, 21, 11, 11, 3, 3, 2, 2, 2, 1] 31 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 73 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: REAL300000220335 none CC1=CC(F)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 7, 7, 21, 21, 21, 21, 21, 31, 31, 31, 21, 21, 21, 2, 2, 2, 1, 1, 1, 7, 7, 31, 31, 21, 21, 21, 19] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220335 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220335 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220335/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220335 Building REAL300000220336 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220336' /scratch/stefan/7769890/working/building/REAL300000220336 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220336 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220336/0 /scratch/stefan/7769890/working/building/REAL300000220336 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/339 `/scratch/stefan/7769890/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CN=C2Cl)N1) `REAL300000220336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220336 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CN=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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, 31, 31, 31, 23, 23, 23, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 31, 31, 9, 9, 1, 1, 1, 21] 31 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 89 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: REAL300000220336 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CN=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 23, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 3, 11, 11, 23, 23, 23, 1] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 69 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220336 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220336 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220336/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220336 Building REAL300000220337 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220337' /scratch/stefan/7769890/working/building/REAL300000220337 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220337 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220337/0 /scratch/stefan/7769890/working/building/REAL300000220337 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/340 `/scratch/stefan/7769890/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)OC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC) `REAL300000220337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220337 none CCC(C)OC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 134, 111, 134, 36, 36, 36, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 36, 36, 36, 36, 88, 135, 135, 135, 135, 135, 134, 134, 134, 134, 36, 12, 12, 2, 2, 2, 3, 3, 1, 36, 36, 88, 88, 88] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 405 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220337 none CCC(C)OC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 11, 7, 11, 1, 1, 1, 1, 1, 5, 5, 36, 36, 36, 36, 36, 64, 104, 104, 36, 36, 36, 1, 1, 1, 1, 3, 12, 12, 12, 12, 12, 11, 11, 11, 11, 1, 5, 5, 36, 36, 36, 64, 64, 36, 1, 1, 4, 4, 4] 201 rigid atoms, others: [36, 5, 6, 7, 8, 45, 46, 25, 22, 23, 24, 4] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 417 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220337 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220337 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220337/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220337 Building REAL300000220338 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220338' /scratch/stefan/7769890/working/building/REAL300000220338 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220338 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220338/0 /scratch/stefan/7769890/working/building/REAL300000220338 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/341 `/scratch/stefan/7769890/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N=C(Cl)N2C)=N1) `REAL300000220338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220338 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N=C(Cl)N2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 16, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [40, 40, 40, 40, 49, 49, 49, 40, 40, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 49, 49, 40, 9, 9, 2, 2, 2] 49 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 118 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: REAL300000220338 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N=C(Cl)N2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 16, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 40, 40, 40, 40, 40, 40, 40, 1, 2, 2, 2, 3, 3, 1, 9, 9, 40, 40, 40] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 82 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220338 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220338 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220338/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220338 Building REAL300000220339 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220339' /scratch/stefan/7769890/working/building/REAL300000220339 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220339 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220339/0 /scratch/stefan/7769890/working/building/REAL300000220339 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/342 `/scratch/stefan/7769890/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CS2)N1) `REAL300000220339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220339 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [61, 61, 60, 60, 86, 104, 104, 60, 60, 60, 12, 12, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 60, 61, 61, 61, 86, 86, 12, 12, 7, 7, 1, 7, 7, 1, 61] 126 rigid atoms, others: [37, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 330 number of broken/clashed sets: 125 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220339 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 60, 60, 60, 109, 109, 61, 109, 109, 60, 60, 1, 2, 2, 2, 3, 3, 11, 11, 109, 109, 61, 109, 109, 60, 1] 126 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 307 number of broken/clashed sets: 125 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220339 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [109, 109, 109, 109, 126, 126, 126, 109, 109, 109, 49, 49, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 109, 109, 109, 109, 126, 126, 49, 49, 1, 1, 1, 1, 1, 7, 109] 126 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 291 number of broken/clashed sets: 125 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220339 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220339 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220339/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220339 Building REAL300000220340 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220340' /scratch/stefan/7769890/working/building/REAL300000220340 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220340 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220340/0 /scratch/stefan/7769890/working/building/REAL300000220340 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/343 `/scratch/stefan/7769890/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1C) `REAL300000220340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220340 none CCN1N=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', '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, 8, 8, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [80, 45, 45, 45, 45, 45, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 45, 45, 80, 80, 80, 80, 80, 45, 45, 45, 11, 11, 3, 3, 2, 2, 2, 1, 45, 45, 45] 106 rigid atoms, others: [38, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 278 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220340 none CCN1N=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', '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, 8, 8, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 45, 45, 45, 45, 45, 75, 76, 76, 45, 45, 45, 1, 1, 6, 6, 6, 6, 6, 2, 2, 2, 7, 7, 75, 75, 45, 45, 45, 45, 2, 2, 2] 106 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220340 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220340 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220340/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220340 Building REAL300000220341 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220341' /scratch/stefan/7769890/working/building/REAL300000220341 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220341 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220341/0 /scratch/stefan/7769890/working/building/REAL300000220341 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/344 `/scratch/stefan/7769890/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCCCC#N)=C2)=N1) `REAL300000220341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220341 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCCCC#N)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 49, 74, 74, 27, 27, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 7, 13, 13, 13, 1, 27, 27, 27, 27, 49, 49, 27, 5, 5, 1, 1, 1, 7, 7, 13, 13, 13, 13, 1] 201 rigid atoms, others: [34, 35, 36, 43, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 316 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220341 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCCCC#N)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 27, 27, 75, 82, 147, 147, 147, 27, 1, 2, 2, 2, 3, 3, 1, 9, 9, 27, 27, 27, 82, 82, 147, 147, 147, 147, 27] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 513 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220341 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220341 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220341/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220341 Building REAL300000220342 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220342' /scratch/stefan/7769890/working/building/REAL300000220342 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220342 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220342/0 /scratch/stefan/7769890/working/building/REAL300000220342 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/345 `/scratch/stefan/7769890/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC=CC2=CC=CC=C2[N+](=O)[O-])=N1) `REAL300000220342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220342 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC=CC2=CC=CC=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [61, 61, 61, 61, 83, 83, 83, 61, 61, 61, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 61, 61, 61, 61, 83, 83, 61, 13, 13, 7, 7, 1, 1, 1, 1] 83 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 231 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220342 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC=CC2=CC=CC=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 29, 29, 61, 61, 61, 61, 61, 61, 61, 61, 1, 2, 2, 2, 3, 3, 1, 11, 11, 29, 29, 61, 61, 61, 61] 83 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 161 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220342 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220342 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220342/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220342 Building REAL300000220343 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220343' /scratch/stefan/7769890/working/building/REAL300000220343 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220343 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220343/0 /scratch/stefan/7769890/working/building/REAL300000220343 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/346 `/scratch/stefan/7769890/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3O2)N1) `REAL300000220343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220343 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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, 25, 25, 37, 37, 37, 25, 25, 25, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 37, 37, 12, 11, 1, 1, 1, 1, 1, 26] 37 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 119 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: REAL300000220343 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 11, 11, 26, 26, 25, 25, 26, 1] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220343 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220343 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220343/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220343 Building REAL300000220344 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220344' /scratch/stefan/7769890/working/building/REAL300000220344 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220344 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220344/0 /scratch/stefan/7769890/working/building/REAL300000220344 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/347 `/scratch/stefan/7769890/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C([N+](=O)[O-])C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220344 none CCOC1=CC=C([N+](=O)[O-])C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', '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, 1, 8, 11, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 128, 66, 66, 66, 36, 66, 66, 66, 66, 66, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 152, 152, 152, 152, 152, 66, 66, 66, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 470 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220344 none CCOC1=CC=C([N+](=O)[O-])C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', '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, 1, 8, 11, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 66, 66, 66, 66, 66, 118, 162, 162, 66, 66, 66, 24, 24, 24, 24, 24, 1, 1, 1, 9, 9, 66, 66, 66, 118, 118, 66] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 638 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220344 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220344 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220344/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220344 Building REAL300000220345 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220345' /scratch/stefan/7769890/working/building/REAL300000220345 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220345 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220345/0 /scratch/stefan/7769890/working/building/REAL300000220345 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/348 `/scratch/stefan/7769890/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=C(F)C(F)=C2)=N1) `REAL300000220345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220345 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=C(F)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [13, 13, 13, 13, 15, 15, 15, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 15, 15, 13, 4, 4, 1, 1] 15 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 33 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: REAL300000220345 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=C(F)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 13, 13, 13, 9, 9, 13, 13, 13, 1, 2, 2, 2, 3, 3, 1, 9, 9, 13, 13] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 63 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220345 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220345 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220345/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220345 Building REAL300000220346 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220346' /scratch/stefan/7769890/working/building/REAL300000220346 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220346 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220346/0 /scratch/stefan/7769890/working/building/REAL300000220346 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/349 `/scratch/stefan/7769890/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(C(F)(F)F)=C2)=N1) `REAL300000220346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220346 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 24, 24, 24, 33, 33, 33, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 24, 24, 24, 24, 33, 33, 24, 5, 5, 1, 1, 1] 33 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 94 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220346 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 24, 24, 23, 24, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 3, 1, 9, 9, 24, 24, 24] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 70 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220346 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220346 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220346/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220346 Building REAL300000220347 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220347' /scratch/stefan/7769890/working/building/REAL300000220347 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220347 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220347/0 /scratch/stefan/7769890/working/building/REAL300000220347 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/350 `/scratch/stefan/7769890/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N(C)C)C(F)=C2)N1) `REAL300000220347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220347 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N(C)C)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 59, 69, 69, 32, 32, 32, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 1, 32, 32, 32, 32, 59, 59, 6, 6, 1, 1, 7, 7, 7, 7, 7, 7, 1, 32] 69 rigid atoms, others: [32, 39, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 259 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220347 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N(C)C)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 32, 32, 30, 32, 59, 59, 32, 32, 32, 1, 2, 2, 2, 3, 3, 11, 11, 32, 32, 59, 59, 59, 59, 59, 59, 32, 1] 69 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 40, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 180 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220347 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220347 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220347/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220347 Building REAL300000220348 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220348' /scratch/stefan/7769890/working/building/REAL300000220348 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220348 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220348/0 /scratch/stefan/7769890/working/building/REAL300000220348 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/351 `/scratch/stefan/7769890/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C(F)=C2)=N1) `REAL300000220348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220348 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 64, 98, 98, 39, 39, 39, 7, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 39, 39, 39, 39, 64, 64, 39, 7, 7, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1] 116 rigid atoms, others: [45, 35, 36, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 346 number of broken/clashed sets: 116 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220348 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 39, 39, 38, 39, 83, 83, 83, 83, 83, 39, 39, 39, 1, 2, 2, 2, 3, 3, 1, 11, 11, 39, 39, 83, 83, 83, 83, 83, 83, 83, 83, 39] 116 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220348 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCOCC3)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 116, 116, 116, 83, 83, 83, 34, 34, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 83, 83, 83, 83, 116, 116, 83, 34, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9] 116 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45]) total number of confs: 364 number of broken/clashed sets: 116 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220348 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220348 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220348/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220348 Building REAL300000220349 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220349' /scratch/stefan/7769890/working/building/REAL300000220349 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220349 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220349/0 /scratch/stefan/7769890/working/building/REAL300000220349 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/352 `/scratch/stefan/7769890/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl) `REAL300000220349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220349 none C=CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 147, 92, 29, 27, 29, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 29, 29, 155, 155, 155, 147, 147, 29, 29, 9, 9, 2, 2, 2, 3, 3, 1, 29] 201 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 505 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220349 none C=CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 5, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 52, 86, 86, 29, 29, 29, 1, 1, 1, 30, 30, 30, 20, 20, 1, 1, 5, 5, 29, 29, 29, 52, 52, 29, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 40, 22, 23, 24, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 415 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220349 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220349 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220349/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220349 Building REAL300000220350 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220350' /scratch/stefan/7769890/working/building/REAL300000220350 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220350 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220350/0 /scratch/stefan/7769890/working/building/REAL300000220350 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/353 `/scratch/stefan/7769890/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(F)(F)F)=C2)=N1) `REAL300000220350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220350 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 51, 82, 82, 28, 28, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 13, 13, 13, 1, 28, 28, 28, 28, 51, 51, 28, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 323 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220350 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 28, 28, 28, 28, 28, 136, 136, 136, 136, 28, 1, 2, 2, 2, 3, 3, 1, 9, 9, 28, 28, 28, 28] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 204 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220350 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220350 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220350/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220350 Building REAL300000220351 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220351' /scratch/stefan/7769890/working/building/REAL300000220351 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220351 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220351/0 /scratch/stefan/7769890/working/building/REAL300000220351 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/354 `/scratch/stefan/7769890/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C2OC(C)CC2=C1) `REAL300000220351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220351 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C2OC(C)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [75, 52, 52, 52, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 75, 75, 75, 52, 12, 12, 3, 3, 2, 2, 2, 1, 52, 52, 52, 52, 52, 52, 52] 110 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) 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: REAL300000220351 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C2OC(C)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 11, 11, 52, 52, 52, 52, 52, 78, 110, 110, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 11, 11, 78, 78, 52, 52, 52, 52, 1, 2, 2, 2, 1, 1, 1] 110 rigid atoms, others: [1, 2, 3, 4, 5, 38, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 367 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220351 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220351 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220351/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220351 Building REAL300000220352 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220352' /scratch/stefan/7769890/working/building/REAL300000220352 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220352 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220352/0 /scratch/stefan/7769890/working/building/REAL300000220352 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/355 `/scratch/stefan/7769890/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)S2)N1) `REAL300000220352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220352 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [40, 40, 40, 40, 48, 48, 48, 39, 40, 39, 12, 12, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 40, 40, 40, 40, 48, 48, 12, 12, 1, 4, 4, 3, 4, 4, 40] 48 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220352 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 40, 40, 40, 40, 41, 41, 41, 41, 40, 40, 1, 2, 2, 2, 3, 3, 10, 10, 40, 41, 41, 41, 40, 41, 1] 48 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 94 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220352 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CC=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [41, 41, 41, 41, 48, 48, 48, 41, 41, 40, 23, 23, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 41, 41, 41, 41, 48, 48, 23, 23, 3, 1, 1, 1, 1, 1, 41] 48 rigid atoms, others: [33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 122 number of broken/clashed sets: 47 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220352 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220352 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220352/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220352 Building REAL300000220353 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220353' /scratch/stefan/7769890/working/building/REAL300000220353 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220353 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220353/0 /scratch/stefan/7769890/working/building/REAL300000220353 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/356 `/scratch/stefan/7769890/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CCCl)N=C2)=N1) `REAL300000220353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220353 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CCCl)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'Cl', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 16, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 62, 102, 102, 39, 39, 39, 7, 7, 1, 1, 1, 1, 1, 7, 11, 1, 1, 39, 39, 39, 39, 62, 62, 39, 7, 7, 1, 7, 7, 11, 11, 1] 201 rigid atoms, others: [35, 12, 13, 14, 15, 16, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 392 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220353 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CCCl)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'Cl', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 16, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 114, 151, 39, 39, 1, 2, 2, 2, 3, 3, 1, 11, 11, 39, 114, 114, 151, 151, 39] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 607 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220353 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220353 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220353/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220353 Building REAL300000220354 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220354' /scratch/stefan/7769890/working/building/REAL300000220354 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220354 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220354/0 /scratch/stefan/7769890/working/building/REAL300000220354 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/357 `/scratch/stefan/7769890/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CN2)N1) `REAL300000220354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220354 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CN2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 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: [53, 53, 53, 53, 80, 101, 101, 53, 53, 53, 12, 12, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 53, 54, 54, 54, 80, 80, 12, 12, 7, 7, 1, 7, 7, 1, 1, 53] 101 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 340 number of broken/clashed sets: 100 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220354 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CN2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 53, 53, 53, 91, 91, 74, 91, 91, 53, 53, 1, 2, 2, 2, 3, 3, 12, 12, 91, 91, 75, 91, 91, 53, 53, 1] 101 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 216 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220354 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC(C3=CC=CC=C3)=CN2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 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: [91, 91, 91, 91, 101, 101, 101, 91, 91, 91, 46, 46, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 91, 91, 91, 91, 101, 101, 46, 46, 1, 1, 1, 1, 1, 7, 7, 91] 101 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 227 number of broken/clashed sets: 100 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220354 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220354 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220354/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220354 Building REAL300000220355 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220355' /scratch/stefan/7769890/working/building/REAL300000220355 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220355 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220355/0 /scratch/stefan/7769890/working/building/REAL300000220355 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/358 `/scratch/stefan/7769890/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OCC#N)=C2)N1) `REAL300000220355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220355 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OCC#N)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 58, 84, 84, 33, 33, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 1, 33, 33, 33, 33, 58, 58, 5, 5, 1, 1, 1, 13, 13, 1, 33] 201 rigid atoms, others: [32, 33, 36, 12, 13, 14, 15, 16, 17, 18, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 37]) total number of confs: 338 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220355 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OCC#N)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 33, 33, 33, 33, 33, 86, 128, 128, 33, 1, 2, 2, 2, 3, 3, 12, 12, 33, 33, 33, 128, 128, 33, 1] 201 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 395 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220355 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220355 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220355/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220355 Building REAL300000220356 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220356' /scratch/stefan/7769890/working/building/REAL300000220356 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220356 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220356/0 /scratch/stefan/7769890/working/building/REAL300000220356 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/359 `/scratch/stefan/7769890/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=N2)N1) `REAL300000220356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220356 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [33, 33, 32, 32, 43, 43, 43, 32, 32, 32, 10, 10, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 33, 33, 33, 33, 43, 43, 11, 10, 1, 4, 4, 3, 4, 4, 33] 43 rigid atoms, others: [32, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 132 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: REAL300000220356 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 32, 32, 32, 33, 33, 33, 33, 33, 32, 32, 1, 2, 2, 2, 3, 3, 9, 9, 33, 33, 33, 33, 33, 33, 1] 43 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220356 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3=CC=CC=C3)N=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [33, 33, 33, 33, 43, 43, 43, 33, 33, 33, 23, 23, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 33, 33, 33, 33, 43, 43, 23, 23, 4, 1, 1, 1, 1, 1, 33] 43 rigid atoms, others: [33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 124 number of broken/clashed sets: 42 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220356 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220356 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220356/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220356 Building REAL300000220357 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220357' /scratch/stefan/7769890/working/building/REAL300000220357 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220357 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220357/0 /scratch/stefan/7769890/working/building/REAL300000220357 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/360 `/scratch/stefan/7769890/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(C)C#N)C=C2)=N1) `REAL300000220357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220357 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(C)C#N)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 8, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 40, 65, 65, 24, 24, 24, 4, 4, 1, 1, 1, 1, 1, 1, 11, 40, 40, 40, 1, 1, 24, 24, 24, 24, 40, 40, 24, 4, 4, 1, 1, 40, 40, 40, 40, 1, 1] 201 rigid atoms, others: [33, 34, 39, 40, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 356 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220357 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(C)C#N)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 8, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 13, 13, 24, 24, 13, 13, 103, 151, 151, 151, 24, 24, 1, 2, 2, 2, 3, 3, 1, 13, 13, 24, 24, 151, 151, 151, 151, 24, 24] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 470 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220357 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220357 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220357/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220357 Building REAL300000220358 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220358' /scratch/stefan/7769890/working/building/REAL300000220358 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220358 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220358/0 /scratch/stefan/7769890/working/building/REAL300000220358 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/361 `/scratch/stefan/7769890/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=CN2CC(F)(F)F)=N1) `REAL300000220358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220358 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=CN2CC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 60, 61, 61, 103, 134, 134, 61, 61, 61, 10, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 60, 61, 61, 61, 103, 103, 60, 10, 10, 1, 1, 6, 6] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 477 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220358 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=CN2CC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 5, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 61, 61, 61, 61, 61, 141, 141, 141, 141, 1, 2, 2, 2, 3, 3, 1, 12, 12, 61, 61, 141, 141] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 465 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220358 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220358 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220358/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220358 Building REAL300000220359 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220359' /scratch/stefan/7769890/working/building/REAL300000220359 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220359 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220359/0 /scratch/stefan/7769890/working/building/REAL300000220359 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/362 `/scratch/stefan/7769890/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C4OCOC4=C3)=N2)=N1) `REAL300000220359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220359 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C4OCOC4=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [66, 66, 66, 66, 97, 106, 106, 66, 66, 66, 12, 12, 1, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 5, 5, 1, 66, 67, 67, 67, 97, 97, 62, 13, 12, 1, 5, 5, 5, 5, 5] 127 rigid atoms, others: [36, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 330 number of broken/clashed sets: 126 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220359 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C4OCOC4=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 66, 66, 66, 66, 111, 111, 111, 111, 111, 111, 111, 111, 66, 1, 2, 2, 2, 3, 3, 1, 12, 12, 66, 111, 111, 111, 111, 111] 127 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 195 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220359 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=C4OCOC4=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [111, 111, 111, 111, 127, 127, 127, 111, 111, 111, 38, 38, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 111, 111, 111, 111, 127, 127, 109, 38, 38, 5, 1, 1, 1, 1, 1] 127 rigid atoms, others: [37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 278 number of broken/clashed sets: 126 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220359 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220359 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220359/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220359 Building REAL300000220360 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220360' /scratch/stefan/7769890/working/building/REAL300000220360 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220360 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220360/0 /scratch/stefan/7769890/working/building/REAL300000220360 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/363 `/scratch/stefan/7769890/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CS3)=N2)=N1) `REAL300000220360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220360 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CS3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 66, 92, 131, 131, 67, 67, 67, 11, 11, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 67, 67, 67, 67, 92, 92, 61, 11, 11, 1, 12, 12, 12] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 420 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220360 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CS3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 67, 170, 170, 170, 170, 66, 1, 2, 2, 2, 3, 3, 1, 12, 12, 67, 170, 170, 170] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 260 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220360 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CS3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 170, 170, 201, 201, 201, 170, 170, 170, 57, 57, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 170, 170, 170, 170, 201, 201, 168, 57, 56, 12, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 458 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220360 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220360 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220360/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220360 Building REAL300000220361 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220361' /scratch/stefan/7769890/working/building/REAL300000220361 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220361 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220361/0 /scratch/stefan/7769890/working/building/REAL300000220361 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/364 `/scratch/stefan/7769890/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3N=CC=CN23)N1) `REAL300000220361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220361 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3N=CC=CN23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [33, 33, 33, 33, 44, 44, 44, 33, 33, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 44, 44, 11, 11, 1, 1, 1, 1, 33] 44 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 118 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: REAL300000220361 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3N=CC=CN23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 33, 33, 33, 33, 33, 33, 33, 33, 1, 2, 2, 2, 3, 3, 10, 10, 33, 33, 33, 33, 1] 44 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220361 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220361 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220361/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220361 Building REAL300000220362 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220362' /scratch/stefan/7769890/working/building/REAL300000220362 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220362 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220362/0 /scratch/stefan/7769890/working/building/REAL300000220362 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/365 `/scratch/stefan/7769890/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC3=CC=CC=C23)N1) `REAL300000220362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220362 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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: [31, 31, 31, 31, 41, 41, 41, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 41, 41, 9, 9, 1, 1, 1, 1, 1, 1, 31] 41 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 107 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220362 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 9, 9, 31, 31, 31, 31, 31, 31, 1] 41 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 73 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220362 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220362 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220362/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220362 Building REAL300000220363 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220363' /scratch/stefan/7769890/working/building/REAL300000220363 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220363 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220363/0 /scratch/stefan/7769890/working/building/REAL300000220363 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/366 `/scratch/stefan/7769890/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C(Cl)=C2)=N1) `REAL300000220363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220363 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 58, 104, 104, 30, 30, 30, 5, 5, 1, 1, 1, 1, 1, 1, 7, 27, 27, 1, 1, 1, 30, 30, 30, 30, 58, 58, 30, 5, 5, 1, 1, 27, 1] 201 rigid atoms, others: [33, 34, 36, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 475 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220363 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 30, 30, 28, 30, 106, 170, 170, 30, 30, 30, 1, 2, 2, 2, 3, 3, 1, 9, 9, 30, 30, 170, 30] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 539 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220363 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220363 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220363/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220363 Building REAL300000220364 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220364' /scratch/stefan/7769890/working/building/REAL300000220364 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220364 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220364/0 /scratch/stefan/7769890/working/building/REAL300000220364 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/367 `/scratch/stefan/7769890/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)S1) `REAL300000220364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220364 none CCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.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, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [106, 46, 46, 46, 46, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 46, 106, 106, 106, 106, 106, 46, 46, 12, 12, 3, 3, 2, 2, 2, 1] 118 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 375 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220364 none CCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.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, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 12, 12, 46, 46, 46, 46, 46, 60, 72, 72, 46, 46, 46, 1, 9, 9, 9, 8, 8, 1, 1, 12, 12, 60, 60, 46, 46, 46, 46] 118 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 230 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220364 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220364 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220364/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220364 Building REAL300000220365 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220365' /scratch/stefan/7769890/working/building/REAL300000220365 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220365 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220365/0 /scratch/stefan/7769890/working/building/REAL300000220365 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/368 `/scratch/stefan/7769890/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=N1) `REAL300000220365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220365 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [66, 65, 66, 66, 93, 97, 97, 66, 66, 66, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 6, 6, 7, 7, 1, 65, 66, 66, 66, 93, 93, 66, 13, 13, 1, 1, 7, 7, 7, 7] 139 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 300 number of broken/clashed sets: 138 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220365 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 66, 66, 66, 66, 115, 115, 68, 66, 115, 115, 115, 115, 66, 1, 2, 2, 2, 3, 3, 1, 12, 12, 66, 66, 115, 115, 115, 115] 139 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 455 number of broken/clashed sets: 138 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220365 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [115, 115, 115, 115, 139, 139, 139, 115, 115, 115, 49, 49, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 115, 115, 115, 115, 139, 139, 115, 49, 49, 7, 7, 1, 1, 1, 1] 139 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 342 number of broken/clashed sets: 138 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220365 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220365 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220365/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220365 Building REAL300000220366 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220366' /scratch/stefan/7769890/working/building/REAL300000220366 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220366 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220366/0 /scratch/stefan/7769890/working/building/REAL300000220366 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/369 `/scratch/stefan/7769890/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1F) `REAL300000220366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220366 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [17, 16, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 2, 2, 2, 1, 17] 29 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) 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: REAL300000220366 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 5, 5, 17, 17, 17, 17, 17, 29, 29, 29, 17, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 5, 5, 29, 29, 17, 17, 17, 17, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220366 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220366 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220366/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220366 Building REAL300000220367 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220367' /scratch/stefan/7769890/working/building/REAL300000220367 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220367 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220367/0 /scratch/stefan/7769890/working/building/REAL300000220367 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/370 `/scratch/stefan/7769890/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC(Cl)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N1C) `REAL300000220367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220367 none COC1=NC(Cl)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [60, 42, 42, 42, 42, 42, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 42, 42, 60, 60, 60, 11, 11, 2, 2, 2, 3, 3, 1, 42, 42, 42] 79 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 124 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220367 none COC1=NC(Cl)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 1, 1, 1, 1, 1, 8, 8, 42, 42, 42, 42, 42, 72, 79, 79, 42, 42, 42, 1, 1, 7, 7, 7, 8, 8, 42, 42, 42, 72, 72, 42, 2, 2, 2] 79 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 281 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220367 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220367 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220367/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220367 Building REAL300000220368 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220368' /scratch/stefan/7769890/working/building/REAL300000220368 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220368 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220368/0 /scratch/stefan/7769890/working/building/REAL300000220368 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/371 `/scratch/stefan/7769890/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220368 none CC1=CC=CC=C1C1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 43, 43, 44, 44, 44, 71, 76, 76, 44, 44, 44, 1, 7, 7, 7, 7, 2, 7, 7, 1, 1, 1, 6, 6, 71, 71, 44, 44, 44, 44, 1] 152 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 45, 26] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 258 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: REAL300000220368 none CC1=CC=CC=C1C1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 29, 29, 114, 114, 114, 114, 114, 152, 152, 152, 114, 114, 114, 7, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 29, 29, 152, 152, 114, 114, 114, 114, 7] 152 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 407 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220368 none CC1=CC=CC=C1C1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 60, 114, 114, 44, 44, 43, 44, 44, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 44, 114, 114, 114, 114, 80, 114, 114, 43, 44, 44, 12, 12, 3, 3, 2, 2, 2, 1, 44] 152 rigid atoms, others: [44, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45]) total number of confs: 337 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220368 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220368 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220368/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220368 Building REAL300000220369 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220369' /scratch/stefan/7769890/working/building/REAL300000220369 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220369 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220369/0 /scratch/stefan/7769890/working/building/REAL300000220369 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/372 `/scratch/stefan/7769890/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=COC(C3=CC=CC=C3)=N2)N1) `REAL300000220369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220369 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=COC(C3=CC=CC=C3)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [45, 45, 45, 45, 52, 52, 52, 44, 45, 44, 13, 13, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 45, 45, 45, 45, 52, 52, 13, 13, 1, 4, 4, 2, 4, 4, 45] 52 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220369 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=COC(C3=CC=CC=C3)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 45, 45, 45, 45, 46, 46, 46, 46, 46, 45, 1, 2, 2, 2, 3, 3, 11, 11, 45, 46, 46, 46, 46, 46, 1] 52 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220369 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=COC(C3=CC=CC=C3)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [46, 46, 46, 46, 52, 52, 52, 46, 46, 46, 25, 25, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 46, 46, 46, 46, 52, 52, 25, 25, 3, 1, 1, 1, 1, 1, 46] 52 rigid atoms, others: [33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 126 number of broken/clashed sets: 51 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220369 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220369 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220369/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220369 Building REAL300000220370 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220370' /scratch/stefan/7769890/working/building/REAL300000220370 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220370 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220370/0 /scratch/stefan/7769890/working/building/REAL300000220370 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/373 `/scratch/stefan/7769890/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OC(C)(C)CC3=C2)N1) `REAL300000220370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220370 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OC(C)(C)CC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 24, 24, 24, 29, 29, 29, 24, 24, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 29, 29, 6, 6, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 24] 29 rigid atoms, others: [32, 33, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 43]) total number of confs: 79 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220370 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OC(C)(C)CC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 3, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 43, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 70 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220370 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220370 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220370/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220370 Building REAL300000220371 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220371' /scratch/stefan/7769890/working/building/REAL300000220371 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220371 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220371/0 /scratch/stefan/7769890/working/building/REAL300000220371 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/374 `/scratch/stefan/7769890/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1F) `REAL300000220371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220371 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 16, 16, 5, 9, 16, 16, 16, 16, 5, 5, 3, 3, 1, 1, 1, 1, 16, 16] 29 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 73 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: REAL300000220371 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 5, 5, 16, 16, 16, 16, 16, 29, 29, 29, 16, 16, 16, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 29, 29, 16, 16, 16, 16, 1, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220371 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220371 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220371/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220371 Building REAL300000220372 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220372' /scratch/stefan/7769890/working/building/REAL300000220372 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220372 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220372/0 /scratch/stefan/7769890/working/building/REAL300000220372 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/375 `/scratch/stefan/7769890/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(F)=C2F)N1) `REAL300000220372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220372 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(F)=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [39, 39, 39, 39, 43, 43, 43, 39, 39, 39, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 43, 43, 9, 9, 1, 1, 1, 35] 43 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 85 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: REAL300000220372 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(F)=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 3, 3, 11, 11, 39, 39, 39, 1] 43 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 83 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220372 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220372 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220372/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220372 Building REAL300000220373 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220373' /scratch/stefan/7769890/working/building/REAL300000220373 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220373 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220373/0 /scratch/stefan/7769890/working/building/REAL300000220373 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/376 `/scratch/stefan/7769890/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Cl)=C1OC) `REAL300000220373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220373 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Cl', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [85, 52, 52, 52, 52, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 52, 52, 52, 52, 82, 85, 85, 85, 52, 52, 12, 12, 2, 2, 2, 3, 3, 1, 82, 82, 82] 116 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 218 number of broken/clashed sets: 116 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220373 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Cl', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 52, 52, 52, 52, 52, 76, 88, 88, 52, 52, 52, 1, 1, 1, 1, 5, 4, 4, 4, 1, 1, 9, 9, 52, 52, 52, 76, 76, 52, 6, 6, 6] 116 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 283 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220373 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220373 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220373/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220373 Building REAL300000220374 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220374' /scratch/stefan/7769890/working/building/REAL300000220374 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220374 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220374/0 /scratch/stefan/7769890/working/building/REAL300000220374 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/377 `/scratch/stefan/7769890/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220374 none COCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 125, 80, 71, 20, 20, 36, 36, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 36, 36, 140, 140, 140, 125, 125, 80, 80, 36, 36, 11, 11, 2, 2, 2, 3, 3, 1, 36, 36] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 492 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220374 none COCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 10, 6, 4, 1, 1, 1, 1, 1, 1, 5, 5, 36, 36, 36, 36, 36, 60, 100, 100, 36, 36, 36, 1, 1, 22, 22, 22, 10, 10, 6, 6, 1, 1, 5, 5, 36, 36, 36, 60, 60, 36, 1, 1] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 42, 43, 23, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 397 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220374 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220374 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220374/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220374 Building REAL300000220375 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220375' /scratch/stefan/7769890/working/building/REAL300000220375 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220375 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220375/0 /scratch/stefan/7769890/working/building/REAL300000220375 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/378 `/scratch/stefan/7769890/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N=C3C=CSC3=C2)N1) `REAL300000220375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220375 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N=C3C=CSC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 14, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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: [27, 27, 27, 27, 37, 37, 37, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 37, 37, 9, 9, 1, 1, 1, 27] 37 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 105 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: REAL300000220375 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N=C3C=CSC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 14, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 11, 11, 27, 27, 27, 1] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 73 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220375 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220375 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220375/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220375 Building REAL300000220376 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220376' /scratch/stefan/7769890/working/building/REAL300000220376 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220376 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220376/0 /scratch/stefan/7769890/working/building/REAL300000220376 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/379 `/scratch/stefan/7769890/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(C)C)C=C2)=N1) `REAL300000220376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220376 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(C)C)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 37, 59, 59, 24, 24, 24, 4, 4, 1, 1, 1, 1, 1, 1, 7, 19, 24, 30, 1, 1, 24, 24, 24, 24, 37, 37, 24, 4, 4, 1, 1, 19, 19, 30, 30, 30, 30, 30, 30, 30, 1, 1] 201 rigid atoms, others: [33, 34, 44, 45, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 354 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220376 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(C)C)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 13, 13, 24, 24, 13, 13, 70, 120, 133, 141, 24, 24, 1, 2, 2, 2, 3, 3, 1, 13, 13, 24, 24, 120, 120, 141, 141, 141, 141, 141, 141, 141, 24, 24] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 597 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220376 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220376 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220376/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220376 Building REAL300000220377 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220377' /scratch/stefan/7769890/working/building/REAL300000220377 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220377 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220377/0 /scratch/stefan/7769890/working/building/REAL300000220377 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/380 `/scratch/stefan/7769890/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220377 none CC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 54, 54, 54, 53, 53, 94, 102, 102, 54, 54, 54, 11, 11, 11, 11, 1, 11, 11, 1, 1, 11, 11, 94, 94, 54, 54, 54, 54, 11] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 376 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: REAL300000220377 none CC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 45, 45, 123, 123, 123, 123, 123, 201, 201, 201, 123, 123, 123, 1, 2, 2, 2, 1, 1, 1, 11, 11, 45, 45, 201, 201, 123, 123, 123, 123, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 25, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 674 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220377 none CC1=CC=CC(C2=NNC=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 54, 123, 123, 54, 54, 54, 54, 53, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 123, 123, 123, 123, 81, 123, 123, 53, 54, 11, 11, 3, 3, 2, 2, 2, 1, 123] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 411 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220377 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220377 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220377/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220377 Building REAL300000220378 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220378' /scratch/stefan/7769890/working/building/REAL300000220378 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220378 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220378/0 /scratch/stefan/7769890/working/building/REAL300000220378 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/381 `/scratch/stefan/7769890/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1[N+](=O)[O-]) `REAL300000220378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220378 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 3, 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: [50, 10, 10, 33, 33, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 33, 33, 33, 33, 33, 50, 50, 50, 33, 33, 10, 10, 3, 3, 2, 2, 2, 1, 33] 64 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 170 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: REAL300000220378 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 3, 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: [3, 1, 1, 1, 1, 1, 1, 5, 5, 33, 33, 33, 33, 33, 55, 64, 64, 33, 33, 33, 1, 1, 1, 2, 2, 4, 4, 4, 1, 1, 5, 5, 55, 55, 33, 33, 33, 33, 1] 64 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 38, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 224 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220378 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220378 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220378/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220378 Building REAL300000220379 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220379' /scratch/stefan/7769890/working/building/REAL300000220379 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220379 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220379/0 /scratch/stefan/7769890/working/building/REAL300000220379 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/382 `/scratch/stefan/7769890/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC(=O)[O-])=C2)=N1) `REAL300000220379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220379 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 51, 86, 86, 33, 33, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 14, 27, 27, 1, 33, 33, 33, 33, 51, 51, 33, 5, 5, 1, 1, 1, 14, 14, 1] 201 rigid atoms, others: [33, 34, 35, 38, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 375 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220379 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 33, 33, 33, 33, 33, 115, 148, 166, 166, 33, 1, 2, 2, 2, 3, 3, 1, 12, 12, 33, 33, 33, 148, 148, 33] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 441 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220379 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220379 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220379/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220379 Building REAL300000220380 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220380' /scratch/stefan/7769890/working/building/REAL300000220380 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220380 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220380/0 /scratch/stefan/7769890/working/building/REAL300000220380 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/383 `/scratch/stefan/7769890/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(F)(F)F)=CC=C2F)=N1) `REAL300000220380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220380 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(F)(F)F)=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 39, 39, 39, 51, 51, 51, 39, 39, 39, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 39, 39, 39, 39, 51, 51, 39, 11, 11, 1, 1, 1] 51 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 137 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220380 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(F)(F)F)=CC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 39, 39, 39, 17, 39, 39, 39, 1, 2, 2, 2, 3, 3, 1, 11, 11, 39, 39, 39] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 158 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220380 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220380 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220380/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220380 Building REAL300000220381 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220381' /scratch/stefan/7769890/working/building/REAL300000220381 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220381 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220381/0 /scratch/stefan/7769890/working/building/REAL300000220381 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/384 `/scratch/stefan/7769890/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC1=CC=CN=C1) `REAL300000220381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220381 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 24, 24, 15, 15, 87, 136, 136, 136, 136, 136, 24, 24, 24, 24, 9, 9, 2, 2, 2, 3, 3, 1, 24, 24, 136, 136, 136, 136] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 39] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 269 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220381 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 24, 24, 24, 24, 24, 40, 66, 66, 24, 24, 24, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 2, 2, 2, 1, 5, 5, 24, 24, 24, 40, 40, 24, 1, 1, 14, 14, 14, 14] 201 rigid atoms, others: [0, 1, 2, 3, 4, 40, 41, 18, 19, 20, 21, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 259 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220381 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 8, 8, 41, 41, 126, 126, 126, 126, 126, 189, 191, 191, 126, 126, 126, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 41, 41, 126, 126, 126, 189, 189, 126, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 619 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220381 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220381 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220381/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220381 Building REAL300000220382 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220382' /scratch/stefan/7769890/working/building/REAL300000220382 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220382 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220382/0 /scratch/stefan/7769890/working/building/REAL300000220382 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/385 `/scratch/stefan/7769890/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(Cl)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220382 none COC1=CC=CC(Cl)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [62, 54, 54, 54, 21, 54, 54, 54, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 62, 62, 62, 54, 53, 54, 11, 11, 3, 3, 2, 2, 2, 1] 79 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220382 none COC1=CC=CC(Cl)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 54, 54, 54, 54, 54, 79, 79, 79, 54, 54, 54, 4, 4, 4, 1, 1, 1, 9, 9, 79, 79, 54, 54, 54, 54] 79 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220382 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220382 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220382/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220382 Building REAL300000220383 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220383' /scratch/stefan/7769890/working/building/REAL300000220383 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220383 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220383/0 /scratch/stefan/7769890/working/building/REAL300000220383 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/386 `/scratch/stefan/7769890/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220383 none CC1=CC=C(F)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [33, 33, 18, 33, 33, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 33, 33, 33, 33, 33, 33, 9, 9, 3, 3, 2, 2, 2, 1, 33] 43 rigid atoms, others: [34, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 129 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: REAL300000220383 none CC1=CC=C(F)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 33, 33, 33, 33, 33, 43, 43, 43, 33, 33, 33, 1, 2, 2, 2, 1, 1, 11, 11, 43, 43, 33, 33, 33, 31, 1] 43 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220383 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220383 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220383/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220383 Building REAL300000220384 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220384' /scratch/stefan/7769890/working/building/REAL300000220384 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220384 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220384/0 /scratch/stefan/7769890/working/building/REAL300000220384 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/387 `/scratch/stefan/7769890/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC(F)F)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220384 none COC1=CC=C(OC(F)F)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 47, 47, 47, 47, 47, 47, 95, 121, 121, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 47, 75, 75, 75, 47, 47, 121, 11, 11, 2, 2, 2, 3, 3, 1, 47] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 378 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220384 none COC1=CC=C(OC(F)F)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 23, 23, 1, 1, 7, 7, 47, 47, 47, 47, 47, 71, 119, 119, 47, 47, 47, 1, 3, 3, 3, 1, 1, 23, 7, 7, 47, 47, 47, 71, 71, 47, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 10, 11, 25, 29, 30] set([0, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 463 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220384 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220384 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220384/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220384 Building REAL300000220385 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220385' /scratch/stefan/7769890/working/building/REAL300000220385 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220385 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220385/0 /scratch/stefan/7769890/working/building/REAL300000220385 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/388 `/scratch/stefan/7769890/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C(C)C)N=C2)N1) `REAL300000220385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220385 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C(C)C)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 71, 98, 98, 42, 43, 42, 7, 7, 1, 1, 1, 1, 1, 13, 13, 1, 1, 43, 43, 43, 43, 71, 71, 7, 7, 1, 13, 13, 13, 13, 13, 13, 13, 1, 43] 104 rigid atoms, others: [37, 12, 13, 14, 15, 16, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 367 number of broken/clashed sets: 103 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220385 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C(C)C)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 43, 43, 43, 103, 103, 43, 43, 1, 2, 2, 2, 3, 3, 11, 11, 43, 103, 103, 103, 103, 103, 103, 103, 43, 1] 104 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 359 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220385 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220385 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220385/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220385 Building REAL300000220386 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220386' /scratch/stefan/7769890/working/building/REAL300000220386 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220386 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220386/0 /scratch/stefan/7769890/working/building/REAL300000220386 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/389 `/scratch/stefan/7769890/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C1=NC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1)C1CC1) `REAL300000220386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220386 none CC(=O)N(C1=NC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.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, 1, 11, 8, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 107, 148, 43, 42, 42, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 43, 43, 107, 154, 154, 148, 148, 148, 12, 12, 2, 2, 2, 3, 3, 1, 43, 154, 154, 154, 154, 154] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 603 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220386 none CC(=O)N(C1=NC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.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, 1, 11, 8, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 1, 1, 1, 1, 1, 8, 8, 43, 43, 43, 42, 42, 63, 87, 87, 43, 43, 43, 1, 1, 6, 14, 14, 16, 16, 16, 8, 8, 43, 43, 43, 63, 63, 43, 1, 14, 14, 14, 14, 14] 201 rigid atoms, others: [3, 4, 5, 6, 7, 21, 22, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 348 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220386 none CC(=O)N(C1=NC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.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, 1, 11, 8, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 11, 1, 6, 14, 14, 14, 41, 41, 154, 154, 154, 154, 154, 192, 193, 193, 154, 154, 154, 14, 14, 1, 1, 1, 11, 11, 11, 41, 41, 154, 154, 154, 192, 192, 154, 14, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 38, 39, 40, 41, 42, 23, 24, 25] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 493 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220386 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220386 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220386/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220386 Building REAL300000220387 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220387' /scratch/stefan/7769890/working/building/REAL300000220387 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220387 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220387/0 /scratch/stefan/7769890/working/building/REAL300000220387 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/390 `/scratch/stefan/7769890/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(F)F)C=C2)=N1) `REAL300000220387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220387 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 42, 71, 71, 24, 24, 24, 4, 4, 1, 1, 1, 1, 1, 1, 7, 18, 55, 55, 1, 1, 24, 24, 24, 24, 42, 42, 24, 4, 4, 1, 1, 18, 18, 55, 1, 1] 201 rigid atoms, others: [33, 34, 38, 39, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 452 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220387 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 13, 13, 24, 24, 13, 13, 78, 109, 141, 141, 24, 24, 1, 2, 2, 2, 3, 3, 1, 13, 13, 24, 24, 109, 109, 141, 24, 24] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 525 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220387 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220387 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220387/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220387 Building REAL300000220388 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220388' /scratch/stefan/7769890/working/building/REAL300000220388 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220388 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220388/0 /scratch/stefan/7769890/working/building/REAL300000220388 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/391 `/scratch/stefan/7769890/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1) `REAL300000220388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220388 none CC1=CC(F)=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 10, 10, 62, 62, 62, 61, 61, 90, 106, 106, 62, 62, 62, 1, 10, 10, 10, 10, 10, 10, 1, 1, 10, 10, 62, 62, 62, 90, 90, 62] 201 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 331 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220388 none CC1=CC(F)=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 57, 57, 161, 161, 161, 161, 161, 201, 201, 201, 161, 161, 161, 10, 2, 2, 2, 1, 1, 1, 10, 10, 57, 57, 161, 161, 161, 201, 201, 161] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 506 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220388 none CC1=CC(F)=CC=C1C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 161, 161, 161, 161, 62, 62, 62, 62, 13, 13, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 61, 161, 161, 161, 161, 161, 161, 62, 62, 13, 13, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 245 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220388 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220388 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220388/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220388 Building REAL300000220389 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220389' /scratch/stefan/7769890/working/building/REAL300000220389 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220389 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220389/0 /scratch/stefan/7769890/working/building/REAL300000220389 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/392 `/scratch/stefan/7769890/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CC([N+](=O)[O-])=C3)=N2)=N1) `REAL300000220389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220389 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CC([N+](=O)[O-])=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [74, 73, 74, 74, 108, 120, 120, 74, 74, 74, 12, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 5, 5, 5, 1, 73, 74, 74, 74, 108, 108, 64, 12, 12, 1, 5, 5, 1, 5] 141 rigid atoms, others: [36, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40]) total number of confs: 374 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220389 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CC([N+](=O)[O-])=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 74, 74, 74, 74, 116, 116, 74, 116, 116, 116, 116, 116, 74, 1, 2, 2, 2, 3, 3, 1, 11, 11, 74, 116, 116, 74, 116] 141 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 316 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220389 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CC=CC([N+](=O)[O-])=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 141, 141, 141, 116, 116, 116, 33, 33, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 116, 116, 116, 116, 141, 141, 112, 33, 33, 5, 1, 1, 1, 1] 141 rigid atoms, others: [37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 331 number of broken/clashed sets: 140 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220389 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220389 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220389/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220389 Building REAL300000220390 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220390' /scratch/stefan/7769890/working/building/REAL300000220390 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220390 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220390/0 /scratch/stefan/7769890/working/building/REAL300000220390 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/393 `/scratch/stefan/7769890/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=C(F)C=CC=C3F)O2)=N1) `REAL300000220390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220390 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=C(F)C=CC=C3F)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [67, 66, 67, 67, 99, 103, 103, 67, 67, 67, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 7, 7, 7, 1, 66, 67, 67, 67, 99, 99, 67, 13, 13, 1, 1, 7, 1, 7] 148 rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 319 number of broken/clashed sets: 147 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220390 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=C(F)C=CC=C3F)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 67, 123, 123, 123, 67, 123, 123, 123, 67, 1, 2, 2, 2, 3, 3, 1, 12, 12, 67, 67, 123, 67, 123] 148 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 332 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220390 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=C(F)C=CC=C3F)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 123, 147, 147, 147, 123, 123, 123, 54, 54, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 123, 123, 123, 123, 147, 147, 123, 54, 54, 9, 9, 1, 1, 1] 147 rigid atoms, others: [37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 357 number of broken/clashed sets: 146 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220390 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220390 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220390/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220390 Building REAL300000220391 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220391' /scratch/stefan/7769890/working/building/REAL300000220391 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220391 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220391/0 /scratch/stefan/7769890/working/building/REAL300000220391 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/394 `/scratch/stefan/7769890/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N(C)N=C2C2=CC=CC=C2)N1) `REAL300000220391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220391 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N(C)N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [73, 73, 73, 73, 113, 146, 146, 73, 73, 73, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 73, 73, 73, 73, 113, 113, 11, 11, 2, 2, 2, 7, 7, 2, 7, 7, 73] 151 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 487 number of broken/clashed sets: 150 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220391 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N(C)N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 73, 73, 73, 73, 73, 73, 73, 118, 118, 100, 118, 118, 1, 2, 2, 2, 3, 3, 12, 12, 73, 73, 73, 118, 118, 100, 118, 118, 1] 151 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 26, 42] set([4, 5, 6, 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, 41]) total number of confs: 249 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220391 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)N(C)N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [118, 118, 118, 118, 151, 151, 151, 118, 118, 118, 33, 33, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 151, 151, 33, 33, 7, 7, 7, 1, 1, 1, 1, 1, 118] 151 rigid atoms, others: [37, 38, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 382 number of broken/clashed sets: 150 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220391 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220391 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220391/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220391 Building REAL300000220392 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220392' /scratch/stefan/7769890/working/building/REAL300000220392 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220392 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220392/0 /scratch/stefan/7769890/working/building/REAL300000220392 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/395 `/scratch/stefan/7769890/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=N1) `REAL300000220392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220392 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 32, 54, 54, 19, 19, 19, 3, 3, 1, 1, 1, 1, 1, 1, 13, 28, 28, 28, 39, 39, 1, 1, 19, 19, 19, 19, 32, 32, 19, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 303 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220392 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 19, 19, 12, 12, 97, 138, 138, 138, 149, 149, 19, 19, 1, 2, 2, 2, 3, 3, 1, 12, 12, 19, 19, 19, 19] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 460 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220392 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220392 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220392/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220392 Building REAL300000220393 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220393' /scratch/stefan/7769890/working/building/REAL300000220393 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220393 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220393/0 /scratch/stefan/7769890/working/building/REAL300000220393 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/396 `/scratch/stefan/7769890/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)C=C1) `REAL300000220393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220393 none CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 11, 11, 43, 43, 43, 43, 43, 51, 51, 51, 43, 43, 43, 1, 4, 4, 4, 4, 4, 4, 4, 1, 11, 11, 43, 43, 43, 51, 51, 43, 4, 4] 51 rigid atoms, others: [4, 5, 6, 7, 8, 9, 23, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 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: REAL300000220393 none CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 4, 20, 20, 43, 43, 43, 43, 43, 51, 51, 51, 43, 43, 43, 4, 1, 1, 2, 2, 2, 1, 1, 4, 20, 20, 43, 43, 43, 51, 51, 43, 1, 1] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 41, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 131 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220393 none CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11, 11, 2, 2, 2, 3, 3, 1, 43, 43] 51 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 86 number of broken/clashed sets: 50 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220393 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220393 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220393/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220393 Building REAL300000220394 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220394' /scratch/stefan/7769890/working/building/REAL300000220394 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220394 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220394/0 /scratch/stefan/7769890/working/building/REAL300000220394 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/397 `/scratch/stefan/7769890/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(OC(F)F)=C1) `REAL300000220394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220394 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(OC(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 54, 17, 54, 54, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 54, 54, 108, 146, 146, 54, 91, 91, 91, 54, 54, 11, 11, 2, 2, 2, 3, 3, 1, 146, 54] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 587 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220394 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(OC(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 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: [2, 1, 1, 1, 1, 1, 1, 9, 9, 54, 54, 54, 54, 54, 78, 122, 122, 54, 54, 54, 1, 1, 7, 23, 23, 1, 3, 3, 3, 1, 1, 9, 9, 54, 54, 54, 78, 78, 54, 23, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 20, 21, 25, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 466 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220394 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220394 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220394/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220394 Building REAL300000220395 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220395' /scratch/stefan/7769890/working/building/REAL300000220395 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220395 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220395/0 /scratch/stefan/7769890/working/building/REAL300000220395 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/398 `/scratch/stefan/7769890/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3C=CC(Cl)=CN23)N1) `REAL300000220395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220395 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3C=CC(Cl)=CN23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [39, 39, 39, 39, 56, 56, 56, 39, 39, 39, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 56, 56, 12, 12, 1, 1, 1, 1, 39] 56 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 163 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220395 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3C=CC(Cl)=CN23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 3, 3, 11, 11, 39, 39, 39, 39, 1] 56 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220395 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220395 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220395/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220395 Building REAL300000220396 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220396' /scratch/stefan/7769890/working/building/REAL300000220396 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220396 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220396/0 /scratch/stefan/7769890/working/building/REAL300000220396 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/399 `/scratch/stefan/7769890/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC=CC3=CC=CC=C32)N1) `REAL300000220396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220396 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC=CC3=CC=CC=C32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [41, 41, 41, 41, 52, 52, 52, 41, 41, 41, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 52, 52, 10, 10, 1, 1, 1, 1, 1, 1, 41] 52 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 126 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220396 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC=CC3=CC=CC=C32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 3, 3, 12, 12, 41, 41, 41, 41, 41, 41, 1] 52 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220396 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220396 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220396/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220396 Building REAL300000220397 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220397' /scratch/stefan/7769890/working/building/REAL300000220397 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220397 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220397/0 /scratch/stefan/7769890/working/building/REAL300000220397 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/400 `/scratch/stefan/7769890/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C(C)(C)C)S2)=N1) `REAL300000220397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220397 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C(C)(C)C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 38, 38, 38, 50, 63, 63, 38, 38, 38, 11, 11, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 38, 38, 38, 38, 50, 50, 38, 11, 11, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 63 rigid atoms, others: [12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 208 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220397 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C(C)(C)C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 38, 38, 38, 38, 48, 48, 48, 38, 1, 2, 2, 2, 3, 3, 1, 12, 12, 38, 48, 48, 48, 48, 48, 48, 48, 48, 48] 63 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 144 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220397 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220397 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220397/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220397 Building REAL300000220398 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220398' /scratch/stefan/7769890/working/building/REAL300000220398 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220398 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220398/0 /scratch/stefan/7769890/working/building/REAL300000220398 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/401 `/scratch/stefan/7769890/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1F) `REAL300000220398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220398 none CCN(CC)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [108, 79, 42, 79, 118, 40, 42, 42, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 42, 42, 42, 108, 108, 108, 108, 108, 118, 118, 118, 118, 118, 42, 42, 12, 12, 2, 2, 2, 3, 3, 1, 42] 151 rigid atoms, others: [45, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46]) total number of confs: 598 number of broken/clashed sets: 151 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220398 none CCN(CC)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 4, 1, 4, 14, 1, 1, 1, 1, 1, 5, 5, 42, 42, 42, 42, 42, 74, 109, 109, 42, 42, 42, 1, 1, 1, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 1, 1, 5, 5, 42, 42, 42, 74, 74, 42, 1] 151 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 46, 23, 24, 25, 37] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 470 number of broken/clashed sets: 151 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220398 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220398 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220398/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220398 Building REAL300000220399 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220399' /scratch/stefan/7769890/working/building/REAL300000220399 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220399 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220399/0 /scratch/stefan/7769890/working/building/REAL300000220399 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/402 `/scratch/stefan/7769890/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)N=NN3C)N1) `REAL300000220399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220399 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)N=NN3C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 27, 27, 27, 22, 22, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 27, 27, 7, 7, 1, 1, 1, 2, 2, 2, 22] 27 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 70 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: REAL300000220399 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)N=NN3C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 10, 10, 22, 22, 22, 22, 22, 22, 1] 27 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 63 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220399 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220399 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220399/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220399 Building REAL300000220400 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220400' /scratch/stefan/7769890/working/building/REAL300000220400 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220400 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220400/0 /scratch/stefan/7769890/working/building/REAL300000220400 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/403 `/scratch/stefan/7769890/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2[N+](=O)[O-])=N1) `REAL300000220400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220400 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [31, 31, 31, 31, 41, 41, 41, 31, 31, 31, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 31, 31, 31, 31, 41, 41, 31, 5, 5, 1, 1, 1] 41 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 105 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220400 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 31, 31, 31, 24, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 1, 11, 11, 31, 31, 31] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220400 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220400 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220400/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220400 Building REAL300000220401 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220401' /scratch/stefan/7769890/working/building/REAL300000220401 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220401 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220401/0 /scratch/stefan/7769890/working/building/REAL300000220401 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/404 `/scratch/stefan/7769890/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OC(C)(C)C3)N1) `REAL300000220401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220401 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OC(C)(C)C3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [39, 39, 39, 39, 54, 54, 54, 39, 39, 39, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 54, 54, 12, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 39] 54 rigid atoms, others: [32, 33, 34, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 164 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220401 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OC(C)(C)C3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 3, 3, 10, 10, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1] 54 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 43, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 84 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220401 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220401 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220401/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220401 Building REAL300000220402 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220402' /scratch/stefan/7769890/working/building/REAL300000220402 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220402 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220402/0 /scratch/stefan/7769890/working/building/REAL300000220402 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/405 `/scratch/stefan/7769890/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CN2C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CN=C12) `REAL300000220402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220402 none CC1=CC=CN2C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [33, 33, 33, 33, 33, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 11, 3, 3, 2, 2, 2, 1, 33] 47 rigid atoms, others: [37, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 76 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: REAL300000220402 none CC1=CC=CN2C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 11, 11, 33, 33, 33, 33, 33, 47, 47, 47, 33, 33, 33, 1, 1, 1, 2, 2, 2, 1, 1, 1, 11, 11, 47, 47, 33, 33, 33, 33, 1] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 21, 22, 23, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220402 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220402 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220402/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220402 Building REAL300000220403 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220403' /scratch/stefan/7769890/working/building/REAL300000220403 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220403 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220403/0 /scratch/stefan/7769890/working/building/REAL300000220403 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/406 `/scratch/stefan/7769890/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3C=CC=CN23)N1) `REAL300000220403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220403 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3C=CC=CN23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [31, 31, 31, 31, 47, 47, 47, 31, 31, 31, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 47, 47, 11, 11, 1, 1, 1, 1, 1, 31] 47 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 147 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220403 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3C=CC=CN23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 10, 10, 31, 31, 31, 31, 31, 1] 47 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 78 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220403 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220403 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220403/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220403 Building REAL300000220404 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220404' /scratch/stefan/7769890/working/building/REAL300000220404 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220404 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220404/0 /scratch/stefan/7769890/working/building/REAL300000220404 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/407 `/scratch/stefan/7769890/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C3C=CC(Br)=CN23)=N1) `REAL300000220404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220404 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C3C=CC(Br)=CN23)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 62, 62, 62, 41, 41, 41, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 62, 62, 41, 10, 10, 1, 1, 1, 1] 62 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 185 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220404 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C3C=CC(Br)=CN23)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 3, 3, 1, 11, 11, 41, 41, 41, 41] 62 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 89 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220404 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220404 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220404/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220404 Building REAL300000220405 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220405' /scratch/stefan/7769890/working/building/REAL300000220405 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220405 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220405/0 /scratch/stefan/7769890/working/building/REAL300000220405 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/408 `/scratch/stefan/7769890/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(SC)C=C1OC) `REAL300000220405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220405 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(SC)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 40, 40, 40, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 40, 40, 86, 40, 40, 40, 79, 87, 87, 87, 40, 11, 11, 2, 2, 2, 3, 3, 1, 86, 86, 86, 40, 79, 79, 79] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 307 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220405 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(SC)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 7, 7, 40, 40, 40, 40, 40, 65, 100, 100, 40, 40, 40, 1, 1, 5, 1, 1, 1, 3, 4, 4, 4, 1, 7, 7, 40, 40, 40, 65, 65, 40, 5, 5, 5, 1, 3, 3, 3] 201 rigid atoms, others: [1, 2, 3, 4, 5, 41, 19, 20, 22, 23, 24, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 354 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220405 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220405 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220405/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220405 Building REAL300000220406 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220406' /scratch/stefan/7769890/working/building/REAL300000220406 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220406 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220406/0 /scratch/stefan/7769890/working/building/REAL300000220406 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/409 `/scratch/stefan/7769890/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl) `REAL300000220406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220406 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [39, 24, 22, 24, 24, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 24, 24, 24, 39, 39, 39, 24, 24, 9, 9, 2, 2, 2, 3, 3, 1, 24] 60 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 104 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220406 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 5, 5, 24, 24, 24, 24, 24, 42, 60, 60, 24, 24, 24, 1, 1, 1, 4, 4, 4, 1, 1, 5, 5, 24, 24, 24, 42, 42, 24, 1] 60 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 223 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220406 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220406 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220406/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220406 Building REAL300000220407 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220407' /scratch/stefan/7769890/working/building/REAL300000220407 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220407 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220407/0 /scratch/stefan/7769890/working/building/REAL300000220407 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/410 `/scratch/stefan/7769890/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(C)(C)C)C=C3)O2)=N1) `REAL300000220407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220407 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(C)(C)C)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 67, 68, 68, 99, 139, 139, 68, 68, 68, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 9, 8, 9, 7, 7, 1, 67, 68, 68, 68, 99, 99, 68, 13, 13, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7] 201 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 490 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220407 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(C)(C)C)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 68, 68, 68, 68, 127, 127, 68, 68, 145, 145, 145, 127, 127, 68, 1, 2, 2, 2, 3, 3, 1, 12, 12, 68, 68, 127, 127, 145, 145, 145, 146, 145, 145, 145, 145, 145, 127, 127] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 704 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220407 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(C)(C)C)C=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 160, 201, 201, 127, 127, 127, 45, 45, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 7, 127, 127, 127, 127, 160, 160, 127, 45, 45, 7, 7, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 201 rigid atoms, others: [51, 39, 40, 50, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 574 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220407 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220407 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220407/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220407 Building REAL300000220408 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220408' /scratch/stefan/7769890/working/building/REAL300000220408 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220408 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220408/0 /scratch/stefan/7769890/working/building/REAL300000220408 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/411 `/scratch/stefan/7769890/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC(F)=CC=C3O2)N1) `REAL300000220408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220408 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC(F)=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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, 25, 25, 37, 37, 37, 25, 25, 25, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 37, 37, 9, 9, 1, 1, 1, 1, 26] 37 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 115 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: REAL300000220408 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC(F)=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 11, 11, 26, 26, 25, 26, 1] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 73 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220408 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220408 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220408/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220408 Building REAL300000220409 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220409' /scratch/stefan/7769890/working/building/REAL300000220409 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220409 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220409/0 /scratch/stefan/7769890/working/building/REAL300000220409 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/412 `/scratch/stefan/7769890/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220409 none COCC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 118, 36, 36, 34, 36, 36, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 36, 163, 163, 163, 118, 118, 34, 36, 36, 10, 10, 3, 3, 2, 2, 2, 1, 36] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 495 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: REAL300000220409 none COCC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 36, 36, 36, 36, 36, 62, 105, 105, 36, 36, 36, 1, 24, 24, 24, 8, 8, 1, 1, 1, 5, 5, 62, 62, 36, 36, 36, 36, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 39, 22, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 426 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220409 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220409 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220409/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220409 Building REAL300000220410 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220410' /scratch/stefan/7769890/working/building/REAL300000220410 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220410 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220410/0 /scratch/stefan/7769890/working/building/REAL300000220410 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/413 `/scratch/stefan/7769890/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2OC(F)F)OCO3)=N1) `REAL300000220410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220410 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2OC(F)F)OCO3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 5, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 92, 150, 150, 59, 59, 59, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 44, 44, 1, 1, 1, 59, 59, 59, 59, 92, 92, 56, 9, 9, 1, 1, 44, 1, 1] 201 rigid atoms, others: [35, 36, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37]) total number of confs: 645 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220410 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=C(C=C2OC(F)F)OCO3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 5, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 59, 59, 59, 59, 59, 59, 131, 185, 185, 59, 59, 59, 1, 2, 2, 2, 3, 3, 1, 12, 12, 59, 59, 185, 59, 59] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 514 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220410 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220410 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220410/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220410 Building REAL300000220411 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220411' /scratch/stefan/7769890/working/building/REAL300000220411 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220411 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220411/0 /scratch/stefan/7769890/working/building/REAL300000220411 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/414 `/scratch/stefan/7769890/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1) `REAL300000220411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220411 none CCC1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 1, 12, 12, 1, 1, 1, 1, 1, 1, 11, 11, 60, 60, 60, 59, 59, 94, 128, 128, 60, 60, 60, 1, 12, 12, 13, 13, 13, 13, 13, 12, 12, 1, 1, 11, 11, 60, 60, 60, 94, 94, 60, 12, 12] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 34, 24] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 488 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220411 none CCC1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 56, 56, 165, 165, 165, 164, 164, 201, 201, 201, 165, 165, 165, 12, 1, 1, 2, 2, 2, 2, 2, 1, 1, 12, 12, 56, 56, 165, 165, 165, 201, 201, 165, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 44, 45, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 493 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220411 none CCC1=CC=C(C2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 89, 89, 165, 164, 60, 60, 60, 60, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 59, 165, 165, 165, 165, 165, 165, 165, 165, 165, 60, 60, 12, 12, 2, 2, 2, 3, 3, 1, 165, 165] 201 rigid atoms, others: [43, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 765 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220411 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220411 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220411/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220411 Building REAL300000220412 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220412' /scratch/stefan/7769890/working/building/REAL300000220412 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220412 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220412/0 /scratch/stefan/7769890/working/building/REAL300000220412 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/415 `/scratch/stefan/7769890/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OC2CCCC2)=N1) `REAL300000220412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220412 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OC2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 107, 126, 126, 60, 60, 60, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 60, 60, 60, 60, 107, 107, 60, 9, 9, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 465 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220412 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OC2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 60, 60, 60, 23, 60, 60, 60, 111, 125, 125, 125, 125, 1, 2, 2, 2, 3, 3, 1, 11, 11, 60, 60, 60, 125, 125, 125, 125, 125, 125, 125, 125, 125] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 356 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220412 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OC2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 125, 201, 201, 201, 125, 125, 125, 42, 42, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 201, 201, 125, 42, 42, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 657 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220412 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220412 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220412/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220412 Building REAL300000220413 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220413' /scratch/stefan/7769890/working/building/REAL300000220413 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220413 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220413/0 /scratch/stefan/7769890/working/building/REAL300000220413 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/416 `/scratch/stefan/7769890/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CN=CC=N3)C=C2)=N1) `REAL300000220413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220413 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CN=CC=N3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 35, 53, 53, 19, 19, 19, 3, 3, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 23, 1, 1, 19, 19, 19, 19, 35, 35, 19, 3, 3, 1, 1, 23, 23, 23, 1, 1] 201 rigid atoms, others: [35, 36, 40, 41, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 222 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220413 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CN=CC=N3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 19, 19, 9, 17, 77, 130, 130, 130, 130, 130, 19, 19, 1, 2, 2, 2, 3, 3, 1, 9, 9, 19, 19, 130, 130, 130, 19, 19] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 281 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220413 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CN=CC=N3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 201, 201, 201, 130, 130, 130, 42, 42, 23, 20, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 23, 130, 130, 130, 130, 201, 201, 130, 42, 42, 23, 23, 1, 1, 1, 23, 23] 201 rigid atoms, others: [37, 38, 39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 674 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220413 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220413 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220413/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220413 Building REAL300000220414 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220414' /scratch/stefan/7769890/working/building/REAL300000220414 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220414 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220414/0 /scratch/stefan/7769890/working/building/REAL300000220414 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/417 `/scratch/stefan/7769890/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3CCCC3=C2)N1) `REAL300000220414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220414 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3CCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 27, 27, 27, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 27, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19] 27 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 39]) total number of confs: 79 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: REAL300000220414 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3CCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220414 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220414 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220414/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220414 Building REAL300000220415 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220415' /scratch/stefan/7769890/working/building/REAL300000220415 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220415 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220415/0 /scratch/stefan/7769890/working/building/REAL300000220415 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/418 `/scratch/stefan/7769890/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C#N) `REAL300000220415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220415 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [39, 26, 26, 26, 26, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 26, 26, 26, 26, 39, 39, 39, 26, 26, 10, 10, 3, 3, 1, 1, 1, 1, 26] 67 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) 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: REAL300000220415 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 45, 67, 67, 26, 26, 26, 1, 1, 1, 1, 4, 4, 4, 1, 1, 6, 6, 45, 45, 26, 26, 26, 26, 1] 67 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 27, 28, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 249 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220415 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220415 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220415/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220415 Building REAL300000220416 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220416' /scratch/stefan/7769890/working/building/REAL300000220416 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220416 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220416/0 /scratch/stefan/7769890/working/building/REAL300000220416 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/419 `/scratch/stefan/7769890/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220416 none COCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [89, 72, 23, 23, 43, 43, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 43, 43, 89, 89, 89, 72, 72, 43, 43, 12, 12, 3, 3, 2, 2, 2, 1, 43, 43] 108 rigid atoms, others: [37, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 386 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: REAL300000220416 none COCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [18, 5, 1, 1, 1, 1, 1, 1, 6, 6, 43, 43, 43, 43, 43, 65, 85, 85, 43, 43, 43, 1, 1, 18, 18, 18, 5, 5, 1, 1, 6, 6, 65, 65, 43, 43, 43, 43, 1, 1] 108 rigid atoms, others: [2, 3, 4, 5, 6, 7, 39, 21, 22, 38, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 300 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220416 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220416 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220416/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220416 Building REAL300000220417 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220417' /scratch/stefan/7769890/working/building/REAL300000220417 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220417 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220417/0 /scratch/stefan/7769890/working/building/REAL300000220417 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/420 `/scratch/stefan/7769890/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2Br)=N1) `REAL300000220417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220417 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [37, 37, 37, 37, 43, 43, 43, 37, 37, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 43, 43, 37, 7, 7, 1, 1, 1] 43 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 87 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: REAL300000220417 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 37, 37, 37, 28, 37, 37, 37, 1, 2, 2, 2, 3, 3, 1, 11, 11, 37, 37, 37] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220417 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220417 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220417/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220417 Building REAL300000220418 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220418' /scratch/stefan/7769890/working/building/REAL300000220418 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220418 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220418/0 /scratch/stefan/7769890/working/building/REAL300000220418 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/421 `/scratch/stefan/7769890/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=C1) `REAL300000220418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220418 none CC1=C(C)C=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', '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, 1, 12, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 27, 27, 27, 27, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 27, 27, 27, 28, 28, 28, 28, 28, 28, 27, 11, 11, 3, 3, 2, 2, 2, 1, 27, 27] 41 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 83 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: REAL300000220418 none CC1=C(C)C=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', '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, 1, 12, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 27, 27, 41, 41, 41, 27, 28, 27, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 11, 12, 41, 41, 28, 28, 28, 28, 1, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 40, 22, 23, 24, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220418 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220418 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220418/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220418 Building REAL300000220419 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220419' /scratch/stefan/7769890/working/building/REAL300000220419 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220419 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220419/0 /scratch/stefan/7769890/working/building/REAL300000220419 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/422 `/scratch/stefan/7769890/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220419 none CCOC(=O)COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 146, 146, 49, 146, 49, 15, 15, 25, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 25, 25, 157, 157, 157, 157, 157, 49, 49, 25, 25, 8, 8, 2, 2, 2, 3, 3, 1, 25, 25] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 469 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220419 none CCOC(=O)COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 18, 18, 4, 18, 4, 1, 1, 1, 1, 1, 1, 5, 5, 25, 25, 25, 25, 25, 44, 74, 74, 25, 25, 25, 1, 1, 26, 26, 26, 26, 26, 4, 4, 1, 1, 5, 5, 25, 25, 25, 44, 44, 25, 1, 1] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 44, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 347 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220419 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220419 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220419/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220419 Building REAL300000220420 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220420' /scratch/stefan/7769890/working/building/REAL300000220420 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220420 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220420/0 /scratch/stefan/7769890/working/building/REAL300000220420 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/423 `/scratch/stefan/7769890/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(OC(F)F)C=C1C) `REAL300000220420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220420 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(OC(F)F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 15, 15, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 57, 57, 130, 180, 180, 57, 21, 57, 57, 57, 57, 57, 11, 11, 2, 2, 2, 3, 3, 1, 180, 57, 57, 57, 57] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 619 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220420 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(OC(F)F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 15, 15, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 57, 57, 57, 57, 57, 93, 149, 149, 57, 57, 57, 1, 1, 8, 35, 35, 1, 1, 1, 2, 2, 2, 1, 9, 9, 57, 57, 57, 93, 93, 57, 35, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 39, 18, 19, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 626 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220420 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220420 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220420/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220420 Building REAL300000220421 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220421' /scratch/stefan/7769890/working/building/REAL300000220421 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220421 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220421/0 /scratch/stefan/7769890/working/building/REAL300000220421 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/424 `/scratch/stefan/7769890/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2Cl)=N1) `REAL300000220421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220421 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [15, 15, 15, 15, 27, 27, 27, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 27, 27, 15, 7, 7, 1, 1, 1] 27 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 99 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: REAL300000220421 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 15, 15, 9, 15, 15, 15, 15, 1, 2, 2, 2, 3, 3, 1, 9, 9, 15, 15, 15] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 84 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220421 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220421 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220421/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220421 Building REAL300000220422 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220422' /scratch/stefan/7769890/working/building/REAL300000220422 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220422 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220422/0 /scratch/stefan/7769890/working/building/REAL300000220422 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/425 `/scratch/stefan/7769890/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1N1C=NC=N1) `REAL300000220422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220422 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 31, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 31, 31, 16, 27, 68, 68, 68, 68, 31, 31, 31, 31, 11, 11, 3, 3, 1, 1, 1, 1, 31, 31, 68, 68] 98 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 192 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: REAL300000220422 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 6, 6, 31, 31, 31, 31, 31, 51, 67, 67, 31, 31, 31, 1, 1, 1, 1, 9, 9, 9, 9, 2, 2, 2, 1, 6, 6, 51, 51, 31, 31, 31, 31, 1, 1, 9, 9] 98 rigid atoms, others: [0, 1, 2, 3, 4, 38, 39, 18, 19, 20, 21, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 241 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: REAL300000220422 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 9, 9, 2, 8, 26, 26, 68, 68, 68, 68, 68, 98, 98, 98, 68, 68, 68, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 26, 26, 98, 98, 68, 68, 68, 68, 9, 9, 1, 1] 98 rigid atoms, others: [40, 41, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 317 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220422 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220422 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220422/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220422 Building REAL300000220423 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220423' /scratch/stefan/7769890/working/building/REAL300000220423 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220423 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220423/0 /scratch/stefan/7769890/working/building/REAL300000220423 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/426 `/scratch/stefan/7769890/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220423 none COC1=CC=CC=C1C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [11, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 42, 42, 42, 42, 42, 65, 81, 81, 42, 42, 42, 1, 1, 11, 11, 11, 6, 5, 6, 6, 1, 1, 6, 6, 65, 65, 42, 42, 42, 42, 1, 1] 113 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 45, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 285 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: REAL300000220423 none COC1=CC=CC=C1C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 22, 22, 80, 80, 81, 80, 80, 113, 113, 113, 81, 81, 81, 6, 6, 3, 3, 3, 1, 1, 1, 1, 6, 6, 22, 22, 113, 113, 81, 81, 81, 81, 6, 6] 113 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 341 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: REAL300000220423 none COC1=CC=CC=C1C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [88, 81, 80, 80, 35, 81, 81, 12, 13, 42, 42, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 42, 42, 88, 88, 88, 81, 75, 81, 81, 42, 42, 12, 12, 3, 3, 2, 2, 2, 1, 42, 42] 113 rigid atoms, others: [44, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 368 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220423 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220423 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220423/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220423 Building REAL300000220424 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220424' /scratch/stefan/7769890/working/building/REAL300000220424 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220424 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220424/0 /scratch/stefan/7769890/working/building/REAL300000220424 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/427 `/scratch/stefan/7769890/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=CC(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C2)=C1) `REAL300000220424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220424 none CC1=CC(C)=CC(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 13, 19, 24, 24, 13, 13, 13, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 4, 4, 19, 19, 13, 13, 13, 13, 1, 1, 3] 29 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 46, 47, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 48]) total number of confs: 87 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: REAL300000220424 none CC1=CC(C)=CC(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 3, 3, 1, 1, 8, 8, 21, 21, 21, 21, 21, 29, 29, 29, 21, 21, 21, 3, 3, 1, 2, 2, 2, 1, 2, 2, 2, 1, 3, 3, 8, 8, 29, 29, 21, 21, 21, 21, 3, 3, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 48, 35, 27, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 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: REAL300000220424 none CC1=CC(C)=CC(C2=CC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 20, 20, 20, 8, 7, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 12, 12, 20, 20, 20, 20, 12, 20, 20, 20, 20, 12, 12, 7, 7, 3, 3, 2, 2, 2, 1, 12, 12, 20] 29 rigid atoms, others: [45, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 106 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220424 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220424 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220424/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220424 Building REAL300000220425 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220425' /scratch/stefan/7769890/working/building/REAL300000220425 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220425 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220425/0 /scratch/stefan/7769890/working/building/REAL300000220425 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/428 `/scratch/stefan/7769890/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CO2)C=C1) `REAL300000220425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220425 none CC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 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: [2, 2, 3, 3, 1, 1, 1, 1, 1, 12, 12, 45, 45, 45, 45, 45, 59, 59, 59, 45, 45, 45, 1, 1, 3, 3, 4, 4, 4, 3, 3, 12, 12, 45, 45, 45, 59, 59, 45, 1, 3, 3] 59 rigid atoms, others: [4, 5, 6, 7, 8, 39, 22, 23] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 171 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220425 none CC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 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, 1, 1, 1, 4, 4, 4, 28, 28, 55, 55, 55, 55, 55, 59, 59, 59, 55, 55, 55, 4, 4, 1, 1, 2, 2, 2, 1, 1, 28, 28, 55, 55, 55, 59, 59, 55, 4, 1, 1] 59 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 41, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220425 none CC1=CC=C(C2=NC(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.3', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 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: [51, 51, 51, 51, 45, 45, 45, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 45, 45, 51, 51, 51, 51, 51, 51, 51, 10, 10, 2, 2, 2, 3, 3, 1, 45, 51, 51] 59 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220425 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220425 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220425/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220425 Building REAL300000220426 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220426' /scratch/stefan/7769890/working/building/REAL300000220426 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220426 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220426/0 /scratch/stefan/7769890/working/building/REAL300000220426 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/429 `/scratch/stefan/7769890/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220426 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [73, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 44, 44, 73, 73, 73, 44, 11, 11, 3, 3, 2, 2, 2, 1, 44, 44] 89 rigid atoms, others: [39, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 145 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: REAL300000220426 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 44, 44, 44, 44, 44, 65, 89, 89, 44, 44, 44, 1, 1, 4, 4, 4, 1, 9, 9, 65, 65, 44, 44, 44, 44, 1, 1] 89 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 9, 10, 11, 12, 41, 26, 27, 31] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 297 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220426 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220426 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220426/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220426 Building REAL300000220427 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220427' /scratch/stefan/7769890/working/building/REAL300000220427 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220427 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220427/0 /scratch/stefan/7769890/working/building/REAL300000220427 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/430 `/scratch/stefan/7769890/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CSC=C3)S2)=N1) `REAL300000220427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220427 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CSC=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 14, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [47, 47, 47, 47, 57, 57, 57, 47, 47, 47, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 47, 47, 47, 47, 57, 57, 47, 11, 11, 1, 5, 5, 5] 79 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 135 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220427 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CSC=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 14, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 47, 47, 47, 47, 63, 63, 63, 63, 47, 1, 2, 2, 2, 3, 3, 1, 9, 9, 47, 63, 63, 63] 79 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 120 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220427 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CSC=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 14, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [63, 63, 63, 63, 79, 79, 79, 63, 63, 63, 27, 27, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 63, 63, 63, 63, 79, 79, 63, 27, 27, 5, 1, 1, 1] 79 rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 206 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220427 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220427 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220427/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220427 Building REAL300000220428 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220428' /scratch/stefan/7769890/working/building/REAL300000220428 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220428 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220428/0 /scratch/stefan/7769890/working/building/REAL300000220428 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/431 `/scratch/stefan/7769890/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CN=C3)N=C2)N1) `REAL300000220428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220428 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CN=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [21, 21, 21, 21, 27, 27, 27, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 21, 21, 21, 21, 27, 27, 5, 5, 1, 1, 7, 7, 7, 1, 21] 53 rigid atoms, others: [32, 33, 37, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38]) total number of confs: 74 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: REAL300000220428 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CN=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 21, 41, 41, 41, 41, 21, 21, 1, 2, 2, 2, 3, 3, 9, 9, 21, 21, 41, 41, 41, 21, 1] 53 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 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: REAL300000220428 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(N3C=CN=C3)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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, 41, 41, 41, 53, 53, 53, 41, 41, 41, 13, 13, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 41, 53, 53, 13, 13, 7, 7, 1, 1, 1, 7, 41] 53 rigid atoms, others: [34, 35, 36, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 132 number of broken/clashed sets: 53 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220428 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220428 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220428/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220428 Building REAL300000220429 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220429' /scratch/stefan/7769890/working/building/REAL300000220429 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220429 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220429/0 /scratch/stefan/7769890/working/building/REAL300000220429 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/432 `/scratch/stefan/7769890/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N1) `REAL300000220429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220429 none COC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 4, 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: [130, 130, 76, 130, 76, 76, 76, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 76, 130, 130, 130, 76, 76, 11, 11, 3, 3, 2, 2, 2, 1, 76] 160 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) 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: REAL300000220429 none COC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 4, 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: [13, 13, 1, 13, 1, 1, 1, 1, 1, 12, 12, 76, 76, 76, 76, 76, 113, 124, 124, 76, 76, 76, 1, 13, 13, 13, 1, 1, 12, 12, 113, 113, 77, 77, 77, 76, 1] 160 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 36, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 396 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220429 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220429 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220429/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220429 Building REAL300000220430 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220430' /scratch/stefan/7769890/working/building/REAL300000220430 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220430 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220430/0 /scratch/stefan/7769890/working/building/REAL300000220430 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/433 `/scratch/stefan/7769890/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CN1) `REAL300000220430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220430 none COC(=O)C1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 40, 88, 40, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 40, 40, 88, 88, 88, 40, 9, 9, 3, 3, 1, 1, 1, 1, 40, 40] 115 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: REAL300000220430 none COC(=O)C1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 4, 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: [12, 12, 1, 12, 1, 1, 1, 1, 6, 6, 40, 40, 40, 40, 40, 64, 89, 89, 40, 40, 40, 1, 1, 13, 13, 13, 1, 6, 6, 64, 64, 40, 40, 40, 40, 1, 1] 115 rigid atoms, others: [2, 35, 4, 5, 6, 7, 21, 22, 36, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220430 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220430 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220430/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220430 Building REAL300000220431 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220431' /scratch/stefan/7769890/working/building/REAL300000220431 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220431 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220431/0 /scratch/stefan/7769890/working/building/REAL300000220431 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/434 `/scratch/stefan/7769890/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1) `REAL300000220431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220431 none CCOC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [153, 123, 115, 48, 115, 48, 48, 48, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 48, 153, 153, 153, 153, 153, 49, 49, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 477 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220431 none CCOC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 17, 9, 1, 9, 1, 1, 1, 1, 1, 10, 10, 48, 48, 48, 48, 48, 83, 116, 116, 48, 49, 48, 1, 24, 24, 24, 24, 24, 1, 1, 10, 10, 49, 49, 49, 83, 83, 48] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 23, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 481 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220431 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220431 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220431/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220431 Building REAL300000220432 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220432' /scratch/stefan/7769890/working/building/REAL300000220432 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220432 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220432/0 /scratch/stefan/7769890/working/building/REAL300000220432 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/435 `/scratch/stefan/7769890/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=C([O-])C(F)=C2)N1) `REAL300000220432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220432 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=C([O-])C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 15, 15, 15, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 15, 15, 4, 4, 1, 1, 8] 15 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 57 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: REAL300000220432 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=C([O-])C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 13, 10, 11, 13, 13, 13, 1, 2, 2, 2, 3, 3, 9, 9, 13, 13, 1] 15 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220432 /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `1' /scratch/stefan/7769890/working/building/REAL300000220432/1 /scratch/stefan/7769890/working/building/REAL300000220432 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 1 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/436 `/scratch/stefan/7769890/working/3D/436' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=C(O)C(F)=C2)N1) `REAL300000220432.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220432/1/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: REAL300000220432 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=C(O)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 15, 15, 15, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 15, 15, 7, 7, 1, 2, 1, 13] 30 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 31, 33]) total number of confs: 38 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: REAL300000220432 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=C(O)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 7, 8, 9, 9, 9, 1, 2, 2, 2, 3, 3, 6, 6, 9, 18, 9, 1] 30 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 70 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220432 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220432 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 1: /scratch/stefan/7769890/working/building/REAL300000220432/1.* 0: /scratch/stefan/7769890/working/building/REAL300000220432/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220432 Building REAL300000220433 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220433' /scratch/stefan/7769890/working/building/REAL300000220433 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220433 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220433/0 /scratch/stefan/7769890/working/building/REAL300000220433 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/437 `/scratch/stefan/7769890/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1OC) `REAL300000220433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220433 none COC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [117, 65, 65, 65, 65, 65, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 65, 65, 65, 123, 117, 117, 117, 65, 65, 65, 65, 12, 12, 3, 3, 2, 2, 2, 1, 65, 123, 123, 123] 161 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 295 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: REAL300000220433 none COC1=CC(C)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 65, 65, 65, 65, 65, 103, 133, 133, 65, 65, 65, 1, 1, 1, 3, 4, 4, 4, 1, 2, 2, 2, 9, 9, 103, 103, 65, 65, 65, 64, 1, 4, 4, 4] 161 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 456 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220433 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220433 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220433/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220433 Building REAL300000220434 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220434' /scratch/stefan/7769890/working/building/REAL300000220434 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220434 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220434/0 /scratch/stefan/7769890/working/building/REAL300000220434 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/438 `/scratch/stefan/7769890/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)N=C2)N1) `REAL300000220434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220434 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [20, 20, 20, 20, 25, 25, 25, 20, 20, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 25, 25, 5, 5, 1, 1, 1, 20] 25 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 60 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: REAL300000220434 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 10, 10, 20, 20, 20, 1] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 60 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220434 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220434 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220434/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220434 Building REAL300000220435 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220435' /scratch/stefan/7769890/working/building/REAL300000220435 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220435 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220435/0 /scratch/stefan/7769890/working/building/REAL300000220435 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/439 `/scratch/stefan/7769890/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CS3)S2)=N1) `REAL300000220435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220435 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CS3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 101, 124, 124, 76, 76, 76, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 13, 1, 76, 76, 76, 76, 101, 101, 76, 12, 12, 1, 13, 13, 12] 183 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 360 number of broken/clashed sets: 182 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220435 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CS3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 76, 76, 76, 76, 165, 165, 165, 165, 76, 1, 2, 2, 2, 3, 3, 1, 11, 11, 76, 165, 165, 165] 183 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 262 number of broken/clashed sets: 182 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220435 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CS3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 14, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 183, 183, 183, 165, 165, 165, 85, 85, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 13, 165, 165, 165, 165, 183, 183, 165, 85, 84, 13, 1, 1, 1] 183 rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 420 number of broken/clashed sets: 182 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220435 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220435 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220435/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220435 Building REAL300000220436 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220436' /scratch/stefan/7769890/working/building/REAL300000220436 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220436 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220436/0 /scratch/stefan/7769890/working/building/REAL300000220436 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/440 `/scratch/stefan/7769890/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1Br) `REAL300000220436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220436 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 18, 18, 13, 18, 18, 18, 18, 18, 7, 7, 2, 2, 2, 3, 3, 1, 18, 18] 31 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 82 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: REAL300000220436 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 18, 18, 18, 18, 18, 31, 31, 31, 18, 18, 18, 1, 1, 1, 1, 2, 2, 2, 1, 6, 6, 18, 18, 18, 31, 31, 18, 1, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 115 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220436 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220436 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220436/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220436 Building REAL300000220437 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220437' /scratch/stefan/7769890/working/building/REAL300000220437 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220437 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220437/0 /scratch/stefan/7769890/working/building/REAL300000220437 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/441 `/scratch/stefan/7769890/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C#N)S2)N1) `REAL300000220437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) Killed Solvation calculation failed Skipping REAL300000220437 0 /scratch/stefan/7769890/working/building/REAL300000220437 /scratch/stefan/7769890/working /scratch/stefan/7769890 `0' -> `0.failed' Finished preparing REAL300000220437 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Found failed protomers Marking REAL300000220437 as failed mkdir: created directory `/scratch/stefan/7769890/failed' `/scratch/stefan/7769890/working/building/REAL300000220437' -> `/scratch/stefan/7769890/failed/REAL300000220437' Building REAL300000220438 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220438' /scratch/stefan/7769890/working/building/REAL300000220438 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220438 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220438/0 /scratch/stefan/7769890/working/building/REAL300000220438 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/442 `/scratch/stefan/7769890/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC2=NC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)N21) `REAL300000220438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220438 none CC1=CC=CC2=NC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)N21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 26, 26, 26, 26, 26, 26, 26, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 11, 11, 3, 3, 2, 2, 2, 1] 35 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 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: REAL300000220438 none CC1=CC=CC2=NC=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)N21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 26, 26, 26, 26, 35, 35, 35, 26, 26, 26, 1, 2, 2, 2, 1, 1, 1, 1, 8, 8, 35, 35, 26, 26, 26, 26] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 27, 28, 29, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220438 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220438 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220438/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220438 Building REAL300000220439 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220439' /scratch/stefan/7769890/working/building/REAL300000220439 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220439 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220439/0 /scratch/stefan/7769890/working/building/REAL300000220439 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/443 `/scratch/stefan/7769890/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC([O-])=CC=C2[N+](=O)[O-])N1) `REAL300000220439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220439 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC([O-])=CC=C2[N+](=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 4, 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: [27, 27, 27, 27, 37, 37, 37, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 27, 27, 27, 27, 37, 37, 7, 7, 1, 1, 1, 25] 37 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 105 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: REAL300000220439 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC([O-])=CC=C2[N+](=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 11, 11, 27, 27, 27, 1] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 75 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220439 /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `1' /scratch/stefan/7769890/working/building/REAL300000220439/1 /scratch/stefan/7769890/working/building/REAL300000220439 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 1 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/444 `/scratch/stefan/7769890/working/3D/444' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(O)=CC=C2[N+](=O)[O-])N1) `REAL300000220439.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220439/1/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: REAL300000220439 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(O)=CC=C2[N+](=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [28, 28, 28, 28, 38, 38, 38, 28, 28, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 28, 28, 28, 28, 38, 38, 6, 6, 1, 2, 1, 1, 28] 76 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 35]) total number of confs: 105 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220439 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(O)=CC=C2[N+](=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 2, 2, 2, 3, 3, 11, 11, 28, 56, 28, 28, 1] 76 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 132 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220439 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220439 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 1: /scratch/stefan/7769890/working/building/REAL300000220439/1.* 0: /scratch/stefan/7769890/working/building/REAL300000220439/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220439 Building REAL300000220440 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220440' /scratch/stefan/7769890/working/building/REAL300000220440 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220440 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220440/0 /scratch/stefan/7769890/working/building/REAL300000220440 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/445 `/scratch/stefan/7769890/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3CCCCC3)S2)=N1) `REAL300000220440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220440 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3CCCCC3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 102, 111, 111, 74, 74, 74, 12, 12, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 74, 74, 74, 74, 102, 102, 74, 12, 12, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 329 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220440 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3CCCCC3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 74, 74, 74, 74, 166, 166, 166, 166, 166, 74, 1, 2, 2, 2, 3, 3, 1, 11, 11, 74, 166, 166, 166, 166, 166, 166, 166, 166, 166, 166, 166] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 378 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220440 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3CCCCC3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 166, 201, 201, 201, 166, 166, 166, 75, 75, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 166, 166, 166, 166, 201, 201, 166, 75, 75, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 507 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220440 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220440 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220440/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220440 Building REAL300000220441 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220441' /scratch/stefan/7769890/working/building/REAL300000220441 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220441 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220441/0 /scratch/stefan/7769890/working/building/REAL300000220441 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/446 `/scratch/stefan/7769890/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C#N)=CS2)N1) `REAL300000220441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220441 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C#N)=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [33, 33, 33, 33, 41, 41, 41, 33, 33, 33, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 41, 41, 12, 12, 1, 1, 33] 41 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 103 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220441 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C#N)=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 33, 33, 33, 33, 33, 33, 1, 2, 2, 2, 3, 3, 11, 11, 33, 33, 1] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 77 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220441 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220441 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220441/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220441 Building REAL300000220442 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220442' /scratch/stefan/7769890/working/building/REAL300000220442 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220442 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220442/0 /scratch/stefan/7769890/working/building/REAL300000220442 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/447 `/scratch/stefan/7769890/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CN=C3)S2)N1) `REAL300000220442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220442 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CN=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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: [44, 43, 43, 43, 67, 71, 71, 43, 43, 43, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 1, 43, 44, 44, 44, 67, 67, 11, 11, 1, 5, 5, 4, 5, 44] 91 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 235 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: REAL300000220442 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CN=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 43, 43, 43, 43, 63, 63, 62, 63, 63, 43, 1, 2, 2, 2, 3, 3, 11, 11, 43, 63, 63, 62, 63, 1] 91 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 135 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220442 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CN=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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, 63, 91, 91, 91, 63, 63, 63, 31, 31, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 63, 63, 63, 63, 91, 91, 31, 31, 5, 1, 1, 1, 1, 63] 91 rigid atoms, others: [33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 283 number of broken/clashed sets: 90 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220442 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220442 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220442/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220442 Building REAL300000220443 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220443' /scratch/stefan/7769890/working/building/REAL300000220443 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220443 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220443/0 /scratch/stefan/7769890/working/building/REAL300000220443 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/448 `/scratch/stefan/7769890/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2CC2)N1) `REAL300000220443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220443 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2CC2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 96, 100, 100, 63, 63, 63, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 63, 63, 63, 63, 96, 96, 9, 9, 1, 1, 1, 1, 6, 6, 6, 6, 6, 59] 119 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) total number of confs: 311 number of broken/clashed sets: 119 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220443 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2CC2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 63, 63, 12, 63, 63, 63, 94, 94, 1, 2, 2, 2, 3, 3, 12, 12, 63, 63, 12, 63, 94, 94, 94, 94, 94, 1] 119 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 308 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220443 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2CC2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 119, 119, 119, 94, 94, 94, 32, 32, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 94, 94, 94, 94, 119, 119, 32, 32, 6, 6, 6, 6, 1, 1, 1, 1, 1, 90] 119 rigid atoms, others: [34, 35, 36, 37, 38, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 308 number of broken/clashed sets: 119 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220443 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220443 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220443/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220443 Building REAL300000220444 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220444' /scratch/stefan/7769890/working/building/REAL300000220444 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220444 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220444/0 /scratch/stefan/7769890/working/building/REAL300000220444 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/449 `/scratch/stefan/7769890/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220444 none COCCOC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 139, 86, 53, 24, 24, 24, 14, 24, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 148, 148, 148, 139, 139, 86, 86, 24, 24, 24, 24, 7, 6, 3, 3, 2, 2, 2, 1] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 595 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: REAL300000220444 none COCCOC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 53, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 24, 40, 68, 68, 24, 24, 24, 70, 70, 70, 53, 53, 27, 27, 1, 1, 1, 1, 9, 9, 40, 40, 24, 24, 24, 24] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 494 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220444 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220444 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220444/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220444 Building REAL300000220445 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220445' /scratch/stefan/7769890/working/building/REAL300000220445 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220445 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220445/0 /scratch/stefan/7769890/working/building/REAL300000220445 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/450 `/scratch/stefan/7769890/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC2=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=CC(OC)=C2O1) `REAL300000220445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220445 none COC(=O)C1=CC2=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=CC(OC)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 46, 87, 46, 46, 46, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 46, 46, 46, 46, 74, 46, 46, 87, 87, 87, 46, 11, 11, 3, 3, 2, 2, 2, 1, 46, 46, 74, 74, 74] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 308 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: REAL300000220445 none COC(=O)C1=CC2=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=CC(OC)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 9, 9, 46, 46, 46, 46, 46, 74, 110, 110, 46, 46, 46, 1, 1, 1, 1, 3, 1, 1, 6, 6, 6, 1, 9, 9, 74, 74, 46, 46, 46, 46, 1, 1, 3, 3, 3] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 41, 42, 22, 23, 24, 25, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 391 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220445 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220445 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220445/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220445 Building REAL300000220446 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220446' /scratch/stefan/7769890/working/building/REAL300000220446 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220446 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220446/0 /scratch/stefan/7769890/working/building/REAL300000220446 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/451 `/scratch/stefan/7769890/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(N3C=CC=N3)=C2)N1) `REAL300000220446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220446 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(N3C=CC=N3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [31, 31, 31, 31, 50, 53, 53, 31, 31, 31, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 31, 31, 31, 31, 50, 50, 5, 5, 1, 1, 1, 7, 7, 7, 1, 31] 93 rigid atoms, others: [32, 33, 34, 38, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 39]) total number of confs: 174 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220446 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(N3C=CC=N3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 31, 31, 31, 31, 31, 72, 72, 72, 72, 31, 1, 2, 2, 2, 3, 3, 12, 12, 31, 31, 31, 72, 72, 72, 31, 1] 93 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220446 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(N3C=CC=N3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [72, 72, 72, 72, 93, 93, 93, 72, 72, 72, 23, 23, 7, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 7, 72, 72, 72, 72, 93, 93, 23, 23, 6, 7, 7, 1, 1, 1, 7, 72] 93 rigid atoms, others: [35, 36, 37, 17, 18, 19, 20, 21, 22] set([0, 1, 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, 38, 39]) total number of confs: 248 number of broken/clashed sets: 93 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220446 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220446 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220446/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220446 Building REAL300000220447 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220447' /scratch/stefan/7769890/working/building/REAL300000220447 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220447 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220447/0 /scratch/stefan/7769890/working/building/REAL300000220447 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/452 `/scratch/stefan/7769890/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3CCC3)S2)=N1) `REAL300000220447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220447 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3CCC3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 14, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 83, 108, 108, 60, 60, 60, 12, 12, 1, 1, 1, 1, 1, 1, 13, 13, 13, 1, 60, 60, 60, 60, 83, 83, 60, 12, 12, 1, 13, 13, 13, 13, 13, 13, 13] 166 rigid atoms, others: [12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 348 number of broken/clashed sets: 165 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220447 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3CCC3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 14, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 60, 60, 60, 60, 137, 137, 137, 60, 1, 2, 2, 2, 3, 3, 1, 11, 11, 60, 137, 137, 137, 137, 137, 137, 137] 166 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 330 number of broken/clashed sets: 165 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220447 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3CCC3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 14, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 137, 166, 166, 166, 137, 137, 137, 74, 74, 13, 13, 13, 13, 1, 1, 1, 1, 1, 13, 137, 137, 137, 137, 166, 166, 137, 74, 74, 13, 1, 1, 1, 1, 1, 1, 1] 166 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 431 number of broken/clashed sets: 165 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220447 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220447 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220447/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220447 Building REAL300000220448 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220448' /scratch/stefan/7769890/working/building/REAL300000220448 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220448 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220448/0 /scratch/stefan/7769890/working/building/REAL300000220448 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/453 `/scratch/stefan/7769890/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CN=C1Cl) `REAL300000220448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220448 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CN=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 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: [21, 21, 21, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 9, 9, 2, 2, 2, 3, 3, 1, 21] 29 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34]) total number of confs: 60 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220448 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CN=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 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, 7, 7, 21, 21, 21, 21, 21, 29, 29, 29, 21, 21, 21, 1, 1, 1, 1, 2, 2, 2, 1, 7, 7, 21, 21, 21, 29, 29, 21, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 34, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220448 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220448 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220448/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220448 Building REAL300000220449 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220449' /scratch/stefan/7769890/working/building/REAL300000220449 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220449 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220449/0 /scratch/stefan/7769890/working/building/REAL300000220449 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/454 `/scratch/stefan/7769890/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=CC=CC=C2F)N1) `REAL300000220449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220449 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=CC=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 96, 120, 120, 50, 51, 51, 12, 12, 1, 1, 1, 1, 1, 1, 1, 9, 9, 1, 9, 9, 9, 51, 51, 51, 51, 96, 96, 12, 12, 1, 1, 9, 9, 7, 9, 51] 201 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 465 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220449 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=CC=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 51, 51, 51, 51, 51, 110, 110, 86, 110, 110, 110, 1, 2, 2, 2, 3, 3, 9, 9, 51, 51, 110, 110, 110, 110, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 39] set([4, 5, 6, 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: 308 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220449 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=CC=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 110, 201, 201, 201, 110, 110, 110, 53, 53, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 201, 201, 53, 53, 9, 9, 1, 1, 1, 1, 110] 201 rigid atoms, others: [35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 746 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220449 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220449 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220449/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220449 Building REAL300000220450 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220450' /scratch/stefan/7769890/working/building/REAL300000220450 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220450 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220450/0 /scratch/stefan/7769890/working/building/REAL300000220450 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/455 `/scratch/stefan/7769890/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=C(F)C=C3)C=C2)=N1) `REAL300000220450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220450 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=C(F)C=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 43, 67, 67, 23, 23, 23, 4, 4, 1, 1, 1, 1, 1, 1, 2, 10, 22, 22, 10, 22, 22, 22, 1, 1, 23, 23, 23, 23, 43, 43, 23, 4, 4, 1, 1, 10, 10, 22, 22, 22, 22, 1, 1] 201 rigid atoms, others: [45, 37, 38, 12, 13, 14, 15, 16, 17, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 339 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220450 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=C(F)C=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 13, 13, 23, 23, 23, 23, 42, 102, 163, 163, 108, 163, 163, 163, 23, 23, 1, 2, 2, 2, 3, 3, 1, 13, 13, 23, 23, 102, 102, 163, 163, 163, 163, 23, 23] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 716 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220450 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3=CC=C(F)C=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 201, 201, 201, 163, 163, 163, 47, 47, 22, 22, 22, 22, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 163, 163, 163, 163, 201, 201, 163, 47, 47, 22, 22, 3, 3, 1, 1, 1, 1, 22, 22] 201 rigid atoms, others: [41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46]) total number of confs: 519 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220450 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220450 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220450/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220450 Building REAL300000220451 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220451' /scratch/stefan/7769890/working/building/REAL300000220451 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220451 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220451/0 /scratch/stefan/7769890/working/building/REAL300000220451 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/456 `/scratch/stefan/7769890/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC(Br)=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220451 none CSC1=CC(Br)=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [109, 59, 59, 59, 28, 59, 59, 59, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 109, 109, 109, 59, 59, 59, 11, 11, 2, 2, 2, 3, 3, 1] 124 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 308 number of broken/clashed sets: 124 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220451 none CSC1=CC(Br)=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 59, 59, 59, 59, 59, 93, 107, 107, 59, 59, 59, 10, 10, 10, 1, 1, 1, 10, 10, 59, 59, 59, 93, 93, 59] 124 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 354 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220451 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220451 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220451/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220451 Building REAL300000220452 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220452' /scratch/stefan/7769890/working/building/REAL300000220452 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220452 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220452/0 /scratch/stefan/7769890/working/building/REAL300000220452 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/457 `/scratch/stefan/7769890/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)SC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220452 none CC1=C(Br)SC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 14, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 24, 24, 24, 24, 10, 10, 2, 2, 2, 3, 3, 1, 24] 37 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32]) total number of confs: 63 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: REAL300000220452 none CC1=C(Br)SC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 14, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 24, 37, 37, 37, 24, 24, 24, 1, 2, 2, 2, 9, 9, 24, 24, 24, 37, 37, 24, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 20] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 126 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220452 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220452 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220452/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220452 Building REAL300000220453 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220453' /scratch/stefan/7769890/working/building/REAL300000220453 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220453 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220453/0 /scratch/stefan/7769890/working/building/REAL300000220453 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/458 `/scratch/stefan/7769890/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)SC=C1) `REAL300000220453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220453 none COC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [72, 58, 58, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 58, 58, 58, 72, 72, 72, 9, 9, 3, 3, 2, 2, 2, 1, 58, 58] 90 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) 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: REAL300000220453 none COC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 12, 12, 58, 51, 58, 58, 58, 89, 90, 90, 58, 58, 58, 1, 1, 1, 3, 3, 3, 12, 12, 89, 89, 58, 58, 58, 58, 1, 1] 90 rigid atoms, others: [32, 1, 2, 3, 4, 33, 18, 19, 20] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220453 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220453 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220453/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220453 Building REAL300000220454 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220454' /scratch/stefan/7769890/working/building/REAL300000220454 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220454 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220454/0 /scratch/stefan/7769890/working/building/REAL300000220454 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/459 `/scratch/stefan/7769890/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=NNC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220454 none CCOC(=O)C1=NNC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 120, 120, 60, 120, 60, 60, 60, 60, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 149, 149, 149, 148, 148, 58, 60, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 452 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220454 none CCOC(=O)C1=NNC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 60, 60, 60, 60, 60, 104, 129, 129, 60, 60, 60, 15, 15, 15, 14, 14, 1, 1, 9, 9, 61, 61, 61, 104, 104, 60] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 506 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220454 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220454 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220454/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220454 Building REAL300000220455 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220455' /scratch/stefan/7769890/working/building/REAL300000220455 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220455 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220455/0 /scratch/stefan/7769890/working/building/REAL300000220455 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/460 `/scratch/stefan/7769890/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=CC=CC=C2)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220455 none COC1=CC=C(C2=CC=CC=C2)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 25, 25, 128, 128, 128, 128, 128, 180, 201, 201, 128, 128, 128, 9, 9, 9, 3, 3, 1, 1, 1, 1, 1, 3, 25, 25, 180, 180, 128, 128, 128, 128] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 582 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: REAL300000220455 none COC1=CC=C(C2=CC=CC=C2)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 11, 11, 74, 74, 74, 74, 74, 114, 165, 165, 74, 74, 74, 4, 4, 4, 1, 1, 3, 3, 1, 3, 3, 1, 11, 11, 114, 114, 74, 74, 74, 74] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 12, 13, 14, 38, 31] set([0, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 557 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220455 none COC1=CC=C(C2=CC=CC=C2)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 74, 74, 74, 74, 74, 74, 128, 128, 118, 128, 128, 74, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 104, 104, 104, 74, 74, 128, 128, 122, 128, 128, 74, 12, 12, 3, 3, 2, 2, 2, 1] 201 rigid atoms, others: [46, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 323 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220455 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220455 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220455/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220455 Building REAL300000220456 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220456' /scratch/stefan/7769890/working/building/REAL300000220456 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220456 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220456/0 /scratch/stefan/7769890/working/building/REAL300000220456 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/461 `/scratch/stefan/7769890/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C(F)=C2)=N1) `REAL300000220456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220456 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 20, 20, 20, 29, 29, 29, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 29, 29, 20, 7, 7, 1, 1, 1] 29 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 87 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220456 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 1, 9, 9, 20, 20, 20] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 61 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220456 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220456 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220456/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220456 Building REAL300000220457 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220457' /scratch/stefan/7769890/working/building/REAL300000220457 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220457 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220457/0 /scratch/stefan/7769890/working/building/REAL300000220457 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/462 `/scratch/stefan/7769890/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC(F)(F)F)N=C2)=N1) `REAL300000220457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220457 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC(F)(F)F)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 15, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 77, 118, 118, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 50, 51, 51, 51, 77, 77, 50, 6, 6, 1, 9, 9, 1] 201 rigid atoms, others: [32, 35, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 418 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220457 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC(F)(F)F)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 15, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 143, 143, 143, 143, 50, 50, 1, 2, 2, 2, 3, 3, 1, 11, 11, 50, 143, 143, 50] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 460 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220457 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220457 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220457/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220457 Building REAL300000220458 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220458' /scratch/stefan/7769890/working/building/REAL300000220458 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220458 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220458/0 /scratch/stefan/7769890/working/building/REAL300000220458 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/463 `/scratch/stefan/7769890/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3COCC3=C2)N1) `REAL300000220458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220458 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3COCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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: [17, 17, 17, 17, 28, 28, 28, 17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 28, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 17] 28 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 37]) total number of confs: 96 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: REAL300000220458 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3COCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 3, 3, 10, 10, 17, 17, 17, 17, 17, 17, 17, 1] 28 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 58 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220458 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220458 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220458/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220458 Building REAL300000220459 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220459' /scratch/stefan/7769890/working/building/REAL300000220459 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220459 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220459/0 /scratch/stefan/7769890/working/building/REAL300000220459 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/464 `/scratch/stefan/7769890/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(CC(C)C)C=C2)N1) `REAL300000220459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220459 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(CC(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 16, 16, 26, 39, 39, 16, 16, 16, 4, 4, 1, 1, 1, 1, 1, 1, 4, 5, 7, 1, 1, 16, 16, 16, 16, 26, 26, 4, 4, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 1, 1, 16] 76 rigid atoms, others: [32, 42, 43, 12, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 171 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220459 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(CC(C)C)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 16, 16, 10, 10, 45, 48, 65, 16, 16, 1, 2, 2, 2, 3, 3, 10, 10, 16, 16, 45, 45, 65, 65, 65, 65, 65, 65, 65, 16, 16, 1] 76 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 44, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 429 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220459 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220459 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220459/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220459 Building REAL300000220460 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220460' /scratch/stefan/7769890/working/building/REAL300000220460 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220460 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220460/0 /scratch/stefan/7769890/working/building/REAL300000220460 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/465 `/scratch/stefan/7769890/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1N=C(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1C) `REAL300000220460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220460 none CCCN1N=C(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 128, 41, 41, 41, 41, 41, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 41, 41, 144, 144, 144, 144, 144, 128, 128, 41, 41, 41, 10, 10, 2, 2, 2, 3, 3, 1, 41, 41, 41] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 553 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220460 none CCCN1N=C(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 41, 41, 71, 107, 107, 41, 41, 41, 1, 1, 10, 10, 10, 9, 9, 5, 5, 2, 2, 2, 7, 7, 41, 41, 41, 71, 71, 41, 2, 2, 2] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 22, 23] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 432 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220460 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220460 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220460/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220460 Building REAL300000220461 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220461' /scratch/stefan/7769890/working/building/REAL300000220461 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220461 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220461/0 /scratch/stefan/7769890/working/building/REAL300000220461 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/466 `/scratch/stefan/7769890/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220461 none COC(=O)C1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [142, 142, 44, 142, 44, 44, 44, 44, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 44, 142, 142, 142, 44, 44, 44, 12, 12, 3, 3, 2, 2, 2, 1, 44] 173 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 352 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: REAL300000220461 none COC(=O)C1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 44, 44, 44, 44, 44, 74, 82, 82, 44, 44, 44, 1, 12, 12, 12, 1, 1, 1, 5, 5, 74, 74, 44, 44, 44, 44, 1] 173 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 38, 23, 27, 28, 29] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 290 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220461 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220461 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220461/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220461 Building REAL300000220462 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220462' /scratch/stefan/7769890/working/building/REAL300000220462 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220462 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220462/0 /scratch/stefan/7769890/working/building/REAL300000220462 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/467 `/scratch/stefan/7769890/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC3=CC=CC=C3N2C)N1) `REAL300000220462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220462 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC3=CC=CC=C3N2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [22, 22, 22, 22, 29, 29, 29, 21, 22, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 29, 29, 8, 8, 1, 1, 1, 1, 2, 2, 2, 22] 29 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 87 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: REAL300000220462 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC3=CC=CC=C3N2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 11, 11, 22, 22, 22, 22, 22, 22, 22, 1] 29 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220462 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220462 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220462/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220462 Building REAL300000220463 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220463' /scratch/stefan/7769890/working/building/REAL300000220463 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220463 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220463/0 /scratch/stefan/7769890/working/building/REAL300000220463 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/468 `/scratch/stefan/7769890/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(O)=CC=C2Br)=N1) `REAL300000220463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220463 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(O)=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 43, 43, 43, 32, 32, 32, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 43, 43, 32, 7, 7, 1, 2, 1, 1] 86 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31]) total number of confs: 114 number of broken/clashed sets: 86 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220463 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(O)=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 32, 32, 32, 32, 32, 32, 32, 1, 2, 2, 2, 3, 3, 1, 11, 11, 32, 64, 32, 32] 86 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 142 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220463 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220463 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220463/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220463 Building REAL300000220464 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220464' /scratch/stefan/7769890/working/building/REAL300000220464 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220464 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220464/0 /scratch/stefan/7769890/working/building/REAL300000220464 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/469 `/scratch/stefan/7769890/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=C(F)C=CC=C2F)N1) `REAL300000220464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220464 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=C(F)C=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 160, 163, 163, 89, 89, 89, 12, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 2, 6, 6, 6, 89, 89, 89, 89, 160, 160, 12, 12, 1, 1, 6, 4, 6, 89] 186 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 568 number of broken/clashed sets: 185 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220464 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=C(F)C=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 89, 89, 89, 89, 89, 127, 127, 127, 114, 127, 127, 127, 1, 2, 2, 2, 3, 3, 12, 12, 89, 89, 127, 127, 127, 1] 186 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 39, 26] set([4, 5, 6, 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: 270 number of broken/clashed sets: 185 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220464 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNN=C2C2=C(F)C=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [128, 128, 128, 128, 189, 189, 189, 128, 128, 128, 39, 39, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 189, 189, 39, 39, 9, 9, 1, 1, 1, 128] 189 rigid atoms, others: [36, 37, 38, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 569 number of broken/clashed sets: 188 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220464 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220464 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220464/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220464 Building REAL300000220465 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220465' /scratch/stefan/7769890/working/building/REAL300000220465 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220465 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220465/0 /scratch/stefan/7769890/working/building/REAL300000220465 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/470 `/scratch/stefan/7769890/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220465 none CC1=CC(Br)=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 15, 15, 15, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 15, 15, 15, 15, 15, 15, 9, 9, 2, 2, 2, 3, 3, 1] 27 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 84 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: REAL300000220465 none CC1=CC(Br)=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 27, 27, 27, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 7, 15, 15, 15, 27, 27, 15] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220465 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220465 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220465/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220465 Building REAL300000220466 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220466' /scratch/stefan/7769890/working/building/REAL300000220466 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220466 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220466/0 /scratch/stefan/7769890/working/building/REAL300000220466 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/471 `/scratch/stefan/7769890/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=CC=CC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=C2)C=C1) `REAL300000220466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220466 none CC1=CC=C(C2=CC=CC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 48, 70, 70, 27, 27, 27, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 6, 6, 48, 48, 27, 27, 27, 27, 1, 3, 3] 70 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 43, 24] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 261 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: REAL300000220466 none CC1=CC=C(C2=CC=CC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 46, 46, 46, 46, 46, 70, 70, 70, 46, 46, 46, 5, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 16, 16, 70, 70, 46, 46, 46, 46, 5, 1, 1] 70 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 45, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 224 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: REAL300000220466 none CC1=CC=C(C2=CC=CC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [44, 27, 44, 44, 27, 27, 27, 27, 27, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 27, 44, 44, 44, 44, 44, 44, 44, 27, 27, 27, 12, 12, 3, 3, 1, 1, 1, 1, 27, 44, 44] 70 rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45]) total number of confs: 184 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220466 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220466 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220466/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220466 Building REAL300000220467 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220467' /scratch/stefan/7769890/working/building/REAL300000220467 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220467 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220467/0 /scratch/stefan/7769890/working/building/REAL300000220467 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/472 `/scratch/stefan/7769890/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CN=C3)=C2)N1) `REAL300000220467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220467 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CN=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 58, 82, 82, 35, 35, 35, 7, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 35, 35, 35, 35, 58, 58, 7, 7, 1, 1, 1, 5, 5, 5, 5, 1, 35] 141 rigid atoms, others: [33, 34, 35, 40, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 41]) total number of confs: 288 number of broken/clashed sets: 141 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220467 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CN=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 35, 35, 35, 35, 35, 93, 93, 93, 93, 93, 35, 1, 2, 2, 2, 3, 3, 12, 12, 35, 35, 35, 93, 93, 93, 93, 35, 1] 141 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 41, 25] set([4, 5, 6, 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, 39, 40]) total number of confs: 173 number of broken/clashed sets: 141 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220467 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CN=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 141, 141, 141, 93, 93, 93, 21, 21, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 93, 93, 93, 93, 141, 141, 21, 21, 5, 5, 5, 1, 1, 1, 1, 5, 93] 141 rigid atoms, others: [36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 423 number of broken/clashed sets: 141 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220467 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220467 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220467/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220467 Building REAL300000220468 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220468' /scratch/stefan/7769890/working/building/REAL300000220468 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220468 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220468/0 /scratch/stefan/7769890/working/building/REAL300000220468 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/473 `/scratch/stefan/7769890/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C=C2Br)=N1) `REAL300000220468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220468 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [15, 15, 15, 15, 29, 29, 29, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 29, 29, 15, 7, 7, 1, 1, 1] 29 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 111 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220468 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 15, 15, 12, 15, 15, 15, 15, 1, 2, 2, 2, 3, 3, 1, 9, 9, 15, 15, 15] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 69 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220468 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220468 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220468/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220468 Building REAL300000220469 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220469' /scratch/stefan/7769890/working/building/REAL300000220469 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220469 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220469/0 /scratch/stefan/7769890/working/building/REAL300000220469 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/474 `/scratch/stefan/7769890/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(Cl)=C2F)N1) `REAL300000220469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220469 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(Cl)=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 45, 45, 45, 41, 41, 41, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 45, 45, 9, 9, 1, 1, 1, 41] 45 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 83 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220469 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(Cl)=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 41, 41, 36, 41, 41, 41, 41, 1, 2, 2, 2, 3, 3, 11, 11, 41, 41, 41, 1] 45 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 114 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220469 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220469 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220469/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220469 Building REAL300000220470 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220470' /scratch/stefan/7769890/working/building/REAL300000220470 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220470 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220470/0 /scratch/stefan/7769890/working/building/REAL300000220470 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/475 `/scratch/stefan/7769890/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C=C2Cl)N1) `REAL300000220470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220470 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [27, 27, 27, 27, 33, 33, 33, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 33, 33, 9, 9, 1, 1, 1, 26] 33 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 80 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220470 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 27, 27, 21, 23, 27, 27, 27, 1, 2, 2, 2, 3, 3, 11, 11, 27, 27, 27, 1] 33 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 97 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220470 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220470 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220470/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220470 Building REAL300000220471 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220471' /scratch/stefan/7769890/working/building/REAL300000220471 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220471 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220471/0 /scratch/stefan/7769890/working/building/REAL300000220471 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/476 `/scratch/stefan/7769890/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C=C2Br)=N1) `REAL300000220471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220471 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [15, 15, 15, 15, 29, 29, 29, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 29, 29, 15, 7, 7, 1, 1, 1] 29 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 111 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220471 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 15, 15, 9, 15, 15, 15, 15, 1, 2, 2, 2, 3, 3, 1, 9, 9, 15, 15, 15] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 84 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220471 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220471 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220471/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220471 Building REAL300000220472 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220472' /scratch/stefan/7769890/working/building/REAL300000220472 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220472 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220472/0 /scratch/stefan/7769890/working/building/REAL300000220472 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/477 `/scratch/stefan/7769890/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=C(F)C=C2F)=N1) `REAL300000220472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220472 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=C(F)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [25, 25, 25, 25, 39, 39, 39, 25, 25, 25, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 39, 39, 25, 10, 10, 1, 1] 39 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 129 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220472 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=C(F)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 1, 11, 11, 25, 25] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 68 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220472 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220472 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220472/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220472 Building REAL300000220473 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220473' /scratch/stefan/7769890/working/building/REAL300000220473 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220473 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220473/0 /scratch/stefan/7769890/working/building/REAL300000220473 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/478 `/scratch/stefan/7769890/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CC=C2Cl)=N1) `REAL300000220473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220473 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CC=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [37, 37, 37, 37, 43, 43, 43, 37, 37, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 43, 43, 37, 7, 7, 1, 1, 1] 43 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 87 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: REAL300000220473 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CC=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 37, 37, 37, 21, 37, 37, 37, 1, 2, 2, 2, 3, 3, 1, 11, 11, 37, 27, 37] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 130 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220473 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220473 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220473/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220473 Building REAL300000220474 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220474' /scratch/stefan/7769890/working/building/REAL300000220474 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220474 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220474/0 /scratch/stefan/7769890/working/building/REAL300000220474 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/479 `/scratch/stefan/7769890/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2[N+](=O)[O-])=N1) `REAL300000220474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220474 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [29, 29, 29, 29, 37, 37, 37, 29, 29, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 29, 29, 29, 29, 37, 37, 29, 7, 7, 1, 1, 1] 37 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 93 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: REAL300000220474 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 29, 29, 16, 22, 29, 29, 29, 29, 29, 1, 2, 2, 2, 3, 3, 1, 11, 11, 29, 29, 29] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 110 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220474 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220474 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220474/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220474 Building REAL300000220475 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220475' /scratch/stefan/7769890/working/building/REAL300000220475 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220475 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220475/0 /scratch/stefan/7769890/working/building/REAL300000220475 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/480 `/scratch/stefan/7769890/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC(=O)[O-])N=N2)=N1) `REAL300000220475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220475 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC(=O)[O-])N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 95, 135, 135, 61, 61, 61, 12, 12, 1, 1, 1, 1, 1, 8, 19, 19, 1, 1, 60, 61, 61, 61, 95, 95, 61, 13, 12, 1, 8, 8] 176 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 519 number of broken/clashed sets: 175 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220475 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC(=O)[O-])N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 60, 60, 60, 133, 151, 151, 60, 60, 1, 2, 2, 2, 3, 3, 1, 11, 11, 61, 133, 133] 176 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 511 number of broken/clashed sets: 175 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220475 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220475 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220475/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220475 Building REAL300000220476 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220476' /scratch/stefan/7769890/working/building/REAL300000220476 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220476 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220476/0 /scratch/stefan/7769890/working/building/REAL300000220476 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/481 `/scratch/stefan/7769890/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3C=CC=CN3C(C(C)C)=N2)N1) `REAL300000220476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220476 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3C=CC=CN3C(C(C)C)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [54, 54, 53, 53, 89, 97, 97, 43, 53, 53, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 54, 54, 54, 54, 89, 89, 11, 10, 1, 1, 1, 1, 6, 7, 7, 7, 6, 6, 6, 54] 101 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 389 number of broken/clashed sets: 100 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220476 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3C=CC=CN3C(C(C)C)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 53, 54, 54, 54, 53, 53, 53, 53, 77, 77, 53, 1, 2, 2, 2, 3, 3, 12, 12, 54, 54, 54, 53, 77, 77, 77, 77, 77, 77, 77, 1] 101 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 44, 25] set([4, 5, 6, 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, 39, 40, 41, 42, 43]) total number of confs: 239 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220476 /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `1' /scratch/stefan/7769890/working/building/REAL300000220476/1 /scratch/stefan/7769890/working/building/REAL300000220476 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 1 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/482 `/scratch/stefan/7769890/working/3D/482' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3C=CC=CN3C(C(C)C)=[NH+]2)N1) `REAL300000220476.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220476/1/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: REAL300000220476 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3C=CC=CN3C(C(C)C)=[NH+]2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.cat', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 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: [56, 56, 56, 56, 95, 107, 107, 49, 56, 55, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 56, 56, 56, 56, 95, 95, 10, 10, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 56] 109 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 407 number of broken/clashed sets: 108 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220476 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3C=CC=CN3C(C(C)C)=[NH+]2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.cat', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 56, 56, 56, 56, 56, 56, 56, 56, 90, 90, 56, 56, 1, 2, 2, 2, 3, 3, 11, 11, 56, 56, 56, 56, 90, 90, 90, 90, 90, 90, 90, 1] 109 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 45, 26] set([4, 5, 6, 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, 41, 42, 43, 44]) total number of confs: 304 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220476 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220476 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 1: /scratch/stefan/7769890/working/building/REAL300000220476/1.* 0: /scratch/stefan/7769890/working/building/REAL300000220476/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220476 Building REAL300000220477 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220477' /scratch/stefan/7769890/working/building/REAL300000220477 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220477 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220477/0 /scratch/stefan/7769890/working/building/REAL300000220477 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/483 `/scratch/stefan/7769890/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C(C)C)S2)=N1) `REAL300000220477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220477 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C(C)C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 14, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [75, 75, 75, 75, 109, 124, 124, 75, 75, 75, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 1, 75, 75, 75, 75, 109, 109, 75, 12, 12, 1, 12, 13, 13, 13, 13, 13, 13] 137 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 411 number of broken/clashed sets: 136 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220477 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C(C)C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 14, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 75, 75, 75, 75, 125, 125, 75, 1, 2, 2, 2, 3, 3, 1, 11, 11, 75, 125, 125, 125, 125, 125, 125, 125] 137 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 383 number of broken/clashed sets: 136 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220477 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220477 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220477/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220477 Building REAL300000220478 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220478' /scratch/stefan/7769890/working/building/REAL300000220478 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220478 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220478/0 /scratch/stefan/7769890/working/building/REAL300000220478 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/484 `/scratch/stefan/7769890/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(OC(F)F)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220478 none CC1=CC=C(OC(F)F)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 22, 56, 56, 56, 117, 170, 170, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 56, 56, 56, 56, 56, 56, 170, 11, 11, 2, 2, 2, 3, 3, 1, 56] 201 rigid atoms, others: [38, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 613 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220478 none CC1=CC=C(OC(F)F)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 33, 33, 1, 1, 9, 9, 56, 56, 56, 56, 56, 90, 140, 140, 56, 56, 56, 1, 2, 2, 2, 1, 1, 33, 9, 9, 56, 56, 56, 90, 90, 56, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 9, 10, 24, 28, 29] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 583 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220478 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220478 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220478/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220478 Building REAL300000220479 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220479' /scratch/stefan/7769890/working/building/REAL300000220479 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220479 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220479/0 /scratch/stefan/7769890/working/building/REAL300000220479 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/485 `/scratch/stefan/7769890/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3S2)N1) `REAL300000220479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220479 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 25, 25, 37, 37, 37, 25, 25, 25, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 37, 37, 12, 11, 1, 1, 1, 1, 1, 26] 37 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 118 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: REAL300000220479 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CC=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 25, 25, 26, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 11, 11, 26, 26, 26, 25, 26, 1] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220479 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220479 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220479/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220479 Building REAL300000220480 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220480' /scratch/stefan/7769890/working/building/REAL300000220480 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220480 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220480/0 /scratch/stefan/7769890/working/building/REAL300000220480 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/486 `/scratch/stefan/7769890/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)OC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220480 none COC(=O)C(C)OC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 131, 80, 131, 50, 80, 15, 15, 25, 25, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 25, 25, 131, 131, 131, 80, 80, 80, 80, 25, 25, 9, 9, 2, 2, 2, 3, 3, 1, 25, 25] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 485 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220480 none COC(=O)C(C)OC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 8, 15, 4, 8, 1, 1, 1, 1, 1, 1, 5, 5, 25, 25, 25, 25, 25, 42, 65, 65, 25, 25, 25, 1, 1, 15, 15, 15, 8, 8, 8, 8, 1, 1, 5, 5, 25, 25, 25, 42, 42, 25, 1, 1] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 44, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 278 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220480 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220480 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220480/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220480 Building REAL300000220481 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220481' /scratch/stefan/7769890/working/building/REAL300000220481 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220481 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220481/0 /scratch/stefan/7769890/working/building/REAL300000220481 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/487 `/scratch/stefan/7769890/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=CC=C3)N=C2C(C)(C)C)=N1) `REAL300000220481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220481 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=CC=C3)N=C2C(C)(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 37, 37, 37, 58, 62, 62, 37, 37, 37, 7, 7, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 2, 2, 2, 37, 37, 37, 37, 58, 58, 37, 7, 7, 1, 4, 4, 2, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3] 62 rigid atoms, others: [37, 12, 13, 14, 15, 16, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 226 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220481 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=CC=C3)N=C2C(C)(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 37, 37, 37, 51, 51, 38, 51, 51, 37, 37, 37, 41, 41, 41, 1, 2, 2, 2, 3, 3, 1, 11, 11, 37, 51, 51, 38, 51, 51, 41, 41, 41, 41, 41, 41, 41, 41, 41] 62 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220481 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=CC=C3)N=C2C(C)(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [51, 51, 51, 51, 62, 62, 62, 51, 51, 51, 18, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 51, 51, 51, 51, 62, 62, 51, 18, 18, 4, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6] 62 rigid atoms, others: [38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220481 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220481 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220481/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220481 Building REAL300000220482 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220482' /scratch/stefan/7769890/working/building/REAL300000220482 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220482 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220482/0 /scratch/stefan/7769890/working/building/REAL300000220482 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/488 `/scratch/stefan/7769890/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)OC3=CC=CC=C32)N1) `REAL300000220482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220482 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)OC3=CC=CC=C32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 12, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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: [39, 39, 39, 39, 51, 51, 51, 38, 39, 39, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 51, 51, 11, 11, 1, 1, 1, 1, 39] 51 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 133 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: REAL300000220482 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)OC3=CC=CC=C32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 12, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 3, 3, 11, 12, 39, 39, 39, 39, 1] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220482 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220482 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220482/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220482 Building REAL300000220483 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220483' /scratch/stefan/7769890/working/building/REAL300000220483 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220483 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220483/0 /scratch/stefan/7769890/working/building/REAL300000220483 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/489 `/scratch/stefan/7769890/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1F) `REAL300000220483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220483 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 29, 29, 29, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 29, 29, 29, 42, 42, 42, 29, 12, 12, 3, 3, 2, 2, 2, 1, 29, 29] 57 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 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: 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: REAL300000220483 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 43, 57, 57, 29, 29, 29, 1, 1, 1, 1, 4, 4, 4, 1, 6, 6, 43, 43, 29, 29, 29, 29, 1, 1] 57 rigid atoms, others: [1, 2, 3, 4, 5, 35, 19, 20, 21, 22, 36, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 191 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220483 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220483 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220483/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220483 Building REAL300000220484 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220484' /scratch/stefan/7769890/working/building/REAL300000220484 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220484 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220484/0 /scratch/stefan/7769890/working/building/REAL300000220484 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/490 `/scratch/stefan/7769890/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C(C)(C)C)N1) `REAL300000220484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220484 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C(C)(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 48, 48, 48, 34, 35, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 35, 35, 35, 35, 48, 48, 8, 8, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 164 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: REAL300000220484 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C(C)(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 35, 35, 35, 35, 35, 35, 37, 37, 37, 1, 2, 2, 2, 3, 3, 11, 11, 35, 35, 35, 35, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1] 50 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 44, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 94 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220484 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220484 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220484/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220484 Building REAL300000220485 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220485' /scratch/stefan/7769890/working/building/REAL300000220485 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220485 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220485/0 /scratch/stefan/7769890/working/building/REAL300000220485 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/491 `/scratch/stefan/7769890/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC(C)C)=C2)=N1) `REAL300000220485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220485 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC(C)C)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 49, 80, 80, 27, 27, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 7, 12, 12, 1, 27, 27, 27, 27, 49, 49, 27, 5, 5, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 12, 12, 1] 201 rigid atoms, others: [33, 34, 35, 45, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 340 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220485 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC(C)C)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 8, 8, 27, 27, 27, 27, 27, 76, 79, 128, 128, 27, 1, 2, 2, 2, 3, 3, 1, 8, 8, 27, 27, 27, 79, 79, 128, 128, 128, 128, 128, 128, 128, 27] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 450 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220485 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220485 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220485/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220485 Building REAL300000220486 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220486' /scratch/stefan/7769890/working/building/REAL300000220486 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220486 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220486/0 /scratch/stefan/7769890/working/building/REAL300000220486 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/492 `/scratch/stefan/7769890/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(F)C=C3Cl)N=N2)=N1) `REAL300000220486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220486 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(F)C=C3Cl)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 16, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 89, 95, 95, 59, 59, 59, 12, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 8, 1, 1, 59, 59, 59, 59, 89, 89, 59, 12, 12, 1, 8, 8, 8] 194 rigid atoms, others: [35, 12, 13, 14, 15, 16, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 304 number of broken/clashed sets: 193 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220486 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(F)C=C3Cl)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 16, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 59, 59, 59, 154, 154, 59, 119, 154, 154, 154, 59, 59, 1, 2, 2, 2, 3, 3, 1, 12, 12, 59, 154, 154, 154] 194 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 525 number of broken/clashed sets: 193 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220486 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(F)C=C3Cl)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 16, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 154, 154, 194, 194, 194, 154, 154, 154, 57, 57, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 154, 154, 154, 154, 194, 194, 154, 57, 57, 8, 1, 1, 1] 194 rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 496 number of broken/clashed sets: 193 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220486 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220486 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220486/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220486 Building REAL300000220487 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220487' /scratch/stefan/7769890/working/building/REAL300000220487 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220487 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220487/0 /scratch/stefan/7769890/working/building/REAL300000220487 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/493 `/scratch/stefan/7769890/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(OC)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220487 none COC1=CC=CC(OC)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [72, 54, 54, 54, 12, 54, 54, 54, 85, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 72, 72, 72, 54, 12, 54, 85, 85, 85, 12, 12, 3, 3, 2, 2, 2, 1] 111 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 263 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: REAL300000220487 none COC1=CC=CC(OC)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 9, 9, 57, 57, 57, 57, 57, 83, 104, 104, 57, 57, 57, 4, 4, 4, 1, 1, 1, 3, 3, 3, 9, 9, 83, 83, 57, 57, 57, 57] 107 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 9, 10, 27, 28, 29] set([0, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 324 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220487 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220487 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220487/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220487 Building REAL300000220488 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220488' /scratch/stefan/7769890/working/building/REAL300000220488 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220488 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220488/0 /scratch/stefan/7769890/working/building/REAL300000220488 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/494 `/scratch/stefan/7769890/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=CS2)N1) `REAL300000220488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220488 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 117, 152, 152, 71, 71, 71, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 71, 71, 71, 71, 117, 117, 10, 10, 1, 2, 2, 2, 13, 13, 13, 71] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 526 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220488 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 71, 71, 71, 71, 71, 71, 153, 153, 153, 153, 1, 2, 2, 2, 3, 3, 11, 11, 71, 71, 71, 71, 153, 153, 153, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 247 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220488 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 153, 201, 201, 201, 153, 153, 153, 60, 60, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 201, 201, 60, 60, 13, 13, 13, 13, 1, 1, 1, 153] 201 rigid atoms, others: [36, 37, 38, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 548 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220488 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220488 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220488/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220488 Building REAL300000220489 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220489' /scratch/stefan/7769890/working/building/REAL300000220489 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220489 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220489/0 /scratch/stefan/7769890/working/building/REAL300000220489 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/495 `/scratch/stefan/7769890/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SC3=CC=CC=C3)C=C2)=N1) `REAL300000220489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220489 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SC3=CC=CC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 26, 27, 27, 49, 76, 76, 27, 27, 27, 4, 4, 1, 1, 1, 1, 1, 1, 13, 44, 44, 13, 44, 44, 1, 1, 26, 27, 27, 27, 49, 49, 27, 4, 4, 1, 1, 44, 44, 13, 44, 44, 1, 1] 201 rigid atoms, others: [35, 36, 42, 43, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 383 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220489 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SC3=CC=CC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 27, 27, 12, 12, 132, 172, 172, 132, 172, 172, 27, 27, 1, 2, 2, 2, 3, 3, 1, 12, 12, 27, 27, 172, 172, 132, 172, 172, 27, 27] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 429 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220489 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SC3=CC=CC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 172, 201, 201, 201, 172, 172, 172, 68, 68, 12, 12, 44, 44, 7, 1, 1, 1, 1, 1, 1, 1, 44, 44, 172, 172, 172, 172, 201, 201, 172, 68, 68, 44, 44, 1, 1, 1, 1, 1, 44, 44] 201 rigid atoms, others: [37, 38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43]) total number of confs: 559 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220489 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220489 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220489/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220489 Building REAL300000220490 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220490' /scratch/stefan/7769890/working/building/REAL300000220490 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220490 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220490/0 /scratch/stefan/7769890/working/building/REAL300000220490 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/496 `/scratch/stefan/7769890/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl) `REAL300000220490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220490 none COC1=CC(Cl)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [63, 32, 31, 45, 45, 45, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 45, 45, 45, 63, 63, 63, 45, 12, 12, 2, 2, 2, 3, 3, 1, 45] 83 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 176 number of broken/clashed sets: 83 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220490 none COC1=CC(Cl)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 45, 45, 45, 45, 45, 67, 83, 83, 45, 45, 45, 1, 1, 1, 4, 4, 4, 1, 7, 7, 45, 45, 45, 67, 67, 45, 1] 83 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 260 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220490 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220490 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220490/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220490 Building REAL300000220491 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220491' /scratch/stefan/7769890/working/building/REAL300000220491 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220491 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220491/0 /scratch/stefan/7769890/working/building/REAL300000220491 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/497 `/scratch/stefan/7769890/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(Cl)=CC=C2F)N1) `REAL300000220491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220491 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(Cl)=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 34, 34, 34, 45, 45, 45, 34, 34, 34, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 45, 45, 11, 11, 1, 1, 1, 32] 45 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 123 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220491 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(Cl)=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 34, 34, 34, 30, 34, 34, 34, 1, 2, 2, 2, 3, 3, 10, 10, 34, 30, 34, 1] 45 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 89 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220491 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220491 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220491/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220491 Building REAL300000220492 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220492' /scratch/stefan/7769890/working/building/REAL300000220492 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220492 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220492/0 /scratch/stefan/7769890/working/building/REAL300000220492 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/498 `/scratch/stefan/7769890/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2Cl)=N1) `REAL300000220492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220492 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [37, 37, 37, 37, 43, 43, 43, 37, 37, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 43, 43, 37, 7, 7, 1, 1, 1] 43 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 87 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: REAL300000220492 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 37, 37, 37, 27, 37, 37, 37, 1, 2, 2, 2, 3, 3, 1, 11, 11, 37, 36, 37] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 126 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220492 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220492 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220492/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220492 Building REAL300000220493 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220493' /scratch/stefan/7769890/working/building/REAL300000220493 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220493 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220493/0 /scratch/stefan/7769890/working/building/REAL300000220493 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/499 `/scratch/stefan/7769890/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Br)=C1) `REAL300000220493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220493 none CC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [15, 15, 15, 15, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 2, 2, 2, 3, 3, 1, 15] 29 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 54 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220493 none CC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 15, 15, 15, 15, 15, 29, 29, 29, 15, 15, 15, 1, 1, 1, 2, 2, 2, 1, 1, 7, 7, 15, 15, 15, 29, 29, 15, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 117 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220493 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220493 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220493/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220493 Building REAL300000220494 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220494' /scratch/stefan/7769890/working/building/REAL300000220494 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220494 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220494/0 /scratch/stefan/7769890/working/building/REAL300000220494 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/500 `/scratch/stefan/7769890/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(F)(F)F)=CC=C2Cl)=N1) `REAL300000220494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220494 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(F)(F)F)=CC=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 38, 38, 38, 45, 45, 45, 38, 38, 38, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 38, 38, 38, 38, 45, 45, 38, 7, 7, 1, 1, 1] 45 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 100 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220494 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(F)(F)F)=CC=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 38, 38, 38, 38, 38, 38, 19, 38, 38, 38, 1, 2, 2, 2, 3, 3, 1, 11, 11, 38, 36, 38] 45 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 155 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220494 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220494 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220494/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220494 Building REAL300000220495 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220495' /scratch/stefan/7769890/working/building/REAL300000220495 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220495 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220495/0 /scratch/stefan/7769890/working/building/REAL300000220495 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/501 `/scratch/stefan/7769890/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC2=CC=CC=C2C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220495 none COC1=NC2=CC=CC=C2C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [57, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 57, 57, 57, 48, 48, 48, 48, 48, 12, 12, 3, 3, 2, 2, 2, 1] 65 rigid atoms, others: [41, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 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: REAL300000220495 none COC1=NC2=CC=CC=C2C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 48, 48, 48, 48, 48, 63, 65, 65, 48, 48, 48, 3, 3, 3, 1, 1, 1, 1, 1, 11, 11, 63, 63, 48, 48, 48, 48] 65 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 33, 29, 30, 31] set([0, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220495 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220495 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220495/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220495 Building REAL300000220496 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220496' /scratch/stefan/7769890/working/building/REAL300000220496 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220496 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220496/0 /scratch/stefan/7769890/working/building/REAL300000220496 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/502 `/scratch/stefan/7769890/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=C(F)C=C3)=C2)=N1) `REAL300000220496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220496 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=C(F)C=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 73, 115, 115, 42, 42, 42, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 5, 9, 9, 9, 9, 9, 9, 1, 42, 42, 42, 42, 73, 73, 42, 6, 6, 1, 1, 1, 5, 5, 9, 9, 9, 9, 1] 201 rigid atoms, others: [37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45]) total number of confs: 426 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220496 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=C(F)C=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 42, 42, 42, 42, 42, 74, 77, 151, 151, 151, 151, 151, 151, 42, 1, 2, 2, 2, 3, 3, 1, 12, 12, 42, 42, 42, 77, 77, 151, 151, 151, 151, 42] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 303 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220496 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OCC3=CC=C(F)C=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 151, 201, 201, 201, 151, 151, 151, 30, 30, 9, 9, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 151, 151, 151, 151, 201, 201, 151, 30, 30, 9, 9, 9, 4, 4, 1, 1, 1, 1, 9] 201 rigid atoms, others: [42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46]) total number of confs: 523 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220496 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220496 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220496/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220496 Building REAL300000220497 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220497' /scratch/stefan/7769890/working/building/REAL300000220497 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220497 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220497/0 /scratch/stefan/7769890/working/building/REAL300000220497 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/503 `/scratch/stefan/7769890/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC=CC2=CC=C(Cl)C=C2)=N1) `REAL300000220497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220497 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC=CC2=CC=C(Cl)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 21, 38, 38, 38, 21, 21, 21, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 21, 22, 22, 22, 38, 38, 21, 5, 5, 3, 3, 1, 1, 1, 1] 38 rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 143 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: REAL300000220497 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC=CC2=CC=C(Cl)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 20, 20, 21, 21, 20, 20, 21, 21, 1, 2, 2, 2, 3, 3, 1, 9, 9, 20, 20, 21, 21, 21, 21] 38 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 81 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220497 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220497 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220497/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220497 Building REAL300000220498 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220498' /scratch/stefan/7769890/working/building/REAL300000220498 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220498 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220498/0 /scratch/stefan/7769890/working/building/REAL300000220498 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/504 `/scratch/stefan/7769890/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3C=CSC3=C2)N1) `REAL300000220498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220498 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3C=CSC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 14, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 27, 27, 27, 23, 23, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 27, 27, 6, 6, 1, 1, 1, 1, 23] 27 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 59 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: REAL300000220498 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C3C=CSC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 14, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 3, 10, 10, 23, 23, 23, 23, 1] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 64 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220498 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220498 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220498/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220498 Building REAL300000220499 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220499' /scratch/stefan/7769890/working/building/REAL300000220499 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220499 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220499/0 /scratch/stefan/7769890/working/building/REAL300000220499 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/505 `/scratch/stefan/7769890/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C(F)=C2)=N1) `REAL300000220499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220499 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 55, 88, 88, 30, 30, 30, 5, 5, 1, 1, 1, 1, 1, 1, 8, 18, 18, 1, 1, 1, 30, 30, 30, 30, 55, 55, 30, 5, 5, 1, 1, 18, 1] 201 rigid atoms, others: [33, 34, 36, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 372 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220499 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 30, 30, 29, 30, 108, 146, 146, 30, 30, 30, 1, 2, 2, 2, 3, 3, 1, 10, 10, 30, 30, 146, 30] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 394 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220499 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220499 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220499/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220499 Building REAL300000220500 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220500' /scratch/stefan/7769890/working/building/REAL300000220500 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220500 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220500/0 /scratch/stefan/7769890/working/building/REAL300000220500 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/506 `/scratch/stefan/7769890/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=C1) `REAL300000220500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220500 none COC1=CC=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [51, 30, 30, 30, 30, 30, 30, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 30, 30, 30, 51, 51, 51, 30, 30, 11, 11, 3, 3, 2, 2, 2, 1, 30, 30] 74 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220500 none COC1=CC=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 30, 30, 30, 30, 30, 53, 74, 74, 30, 30, 30, 1, 1, 1, 2, 2, 2, 1, 1, 11, 11, 53, 53, 31, 31, 31, 30, 1, 1] 74 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 39, 22, 23, 24, 38, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220500 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220500 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220500/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220500 Building REAL300000220501 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220501' /scratch/stefan/7769890/working/building/REAL300000220501 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220501 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220501/0 /scratch/stefan/7769890/working/building/REAL300000220501 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/507 `/scratch/stefan/7769890/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=CC3=CC=CC=C23)N1) `REAL300000220501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220501 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=CC3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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: [29, 29, 29, 29, 41, 41, 41, 29, 29, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 41, 41, 7, 7, 1, 1, 1, 1, 1, 1, 29] 41 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 115 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: REAL300000220501 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=CC3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 2, 2, 2, 3, 3, 9, 9, 29, 29, 29, 29, 29, 29, 1] 41 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 71 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220501 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220501 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220501/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220501 Building REAL300000220502 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220502' /scratch/stefan/7769890/working/building/REAL300000220502 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220502 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220502/0 /scratch/stefan/7769890/working/building/REAL300000220502 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/508 `/scratch/stefan/7769890/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C([N+](=O)[O-])=C2)=N1) `REAL300000220502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220502 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [24, 24, 24, 24, 33, 33, 33, 24, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 24, 24, 24, 24, 33, 33, 24, 7, 7, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220502 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C([N+](=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 24, 24, 17, 17, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 3, 1, 11, 11, 24, 24, 24] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220502 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220502 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220502/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220502 Building REAL300000220503 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220503' /scratch/stefan/7769890/working/building/REAL300000220503 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220503 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220503/0 /scratch/stefan/7769890/working/building/REAL300000220503 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/509 `/scratch/stefan/7769890/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=NC=CN32)N1) `REAL300000220503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220503 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=NC=CN32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [35, 35, 35, 35, 42, 42, 42, 35, 35, 35, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 42, 42, 9, 9, 1, 1, 1, 1, 1, 35] 42 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 94 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: REAL300000220503 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=NC=CN32)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 10, 10, 35, 35, 35, 35, 35, 1] 42 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 78 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220503 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220503 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220503/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220503 Building REAL300000220504 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220504' /scratch/stefan/7769890/working/building/REAL300000220504 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220504 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220504/0 /scratch/stefan/7769890/working/building/REAL300000220504 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/510 `/scratch/stefan/7769890/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SCC3=CC=CC=C3)C=C2)=N1) `REAL300000220504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220504 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SCC3=CC=CC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 29, 49, 49, 17, 17, 17, 3, 3, 1, 1, 1, 1, 1, 1, 9, 32, 34, 34, 32, 34, 34, 1, 1, 17, 17, 17, 17, 29, 29, 17, 3, 3, 1, 1, 32, 32, 34, 34, 32, 34, 34, 1, 1] 201 rigid atoms, others: [45, 36, 37, 12, 13, 14, 15, 16, 17, 46, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 287 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220504 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SCC3=CC=CC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 17, 17, 11, 11, 88, 148, 150, 150, 148, 150, 150, 17, 17, 1, 2, 2, 2, 3, 3, 1, 11, 11, 17, 17, 148, 148, 150, 150, 148, 150, 150, 17, 17] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 493 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220504 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SCC3=CC=CC=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 150, 201, 201, 201, 150, 150, 150, 62, 62, 9, 9, 34, 34, 6, 2, 1, 1, 1, 1, 1, 1, 1, 34, 34, 150, 150, 150, 150, 201, 201, 150, 62, 62, 34, 34, 2, 2, 1, 1, 1, 1, 1, 34, 34] 201 rigid atoms, others: [40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46]) total number of confs: 644 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220504 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220504 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220504/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220504 Building REAL300000220505 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220505' /scratch/stefan/7769890/working/building/REAL300000220505 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220505 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220505/0 /scratch/stefan/7769890/working/building/REAL300000220505 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/511 `/scratch/stefan/7769890/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=CC(C(F)(F)F)=C2)=N1) `REAL300000220505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220505 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=CC(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 22, 22, 22, 33, 33, 33, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 22, 22, 22, 22, 33, 33, 22, 5, 5, 1, 1, 1] 33 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 104 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220505 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=CC(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 1, 9, 9, 22, 22, 22] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 61 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220505 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220505 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220505/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220505 Building REAL300000220506 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220506' /scratch/stefan/7769890/working/building/REAL300000220506 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220506 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220506/0 /scratch/stefan/7769890/working/building/REAL300000220506 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/512 `/scratch/stefan/7769890/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CC=N3)=C2)N1) `REAL300000220506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220506 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CC=N3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 65, 92, 92, 37, 37, 37, 5, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 1, 37, 37, 37, 37, 65, 65, 5, 5, 1, 1, 1, 13, 13, 12, 13, 1, 37] 191 rigid atoms, others: [33, 34, 35, 40, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 41]) total number of confs: 339 number of broken/clashed sets: 191 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220506 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CC=N3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 37, 37, 37, 37, 37, 147, 147, 147, 147, 147, 37, 1, 2, 2, 2, 3, 3, 12, 12, 37, 37, 37, 147, 147, 147, 147, 37, 1] 191 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 41, 25] set([4, 5, 6, 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, 39, 40]) total number of confs: 229 number of broken/clashed sets: 191 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220506 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=CC=N3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 147, 191, 191, 191, 147, 147, 147, 45, 45, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 147, 147, 147, 147, 191, 191, 45, 45, 12, 13, 13, 1, 1, 1, 1, 13, 147] 191 rigid atoms, others: [36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 510 number of broken/clashed sets: 191 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220506 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220506 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220506/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220506 Building REAL300000220507 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220507' /scratch/stefan/7769890/working/building/REAL300000220507 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220507 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220507/0 /scratch/stefan/7769890/working/building/REAL300000220507 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/513 `/scratch/stefan/7769890/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C=C2C(F)(F)F)=N1) `REAL300000220507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220507 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C=C2C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 37, 37, 37, 31, 31, 31, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 31, 31, 31, 31, 37, 37, 31, 5, 5, 1, 1, 1] 37 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 83 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: REAL300000220507 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C=C2C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 31, 31, 17, 21, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 1, 11, 11, 31, 31, 31] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 109 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220507 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220507 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220507/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220507 Building REAL300000220508 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220508' /scratch/stefan/7769890/working/building/REAL300000220508 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220508 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220508/0 /scratch/stefan/7769890/working/building/REAL300000220508 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/514 `/scratch/stefan/7769890/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Br)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1) `REAL300000220508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220508 none COC1=C(Br)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [70, 58, 58, 58, 58, 58, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 58, 70, 70, 70, 58, 9, 9, 2, 2, 2, 3, 3, 1] 81 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 127 number of broken/clashed sets: 80 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220508 none COC1=C(Br)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 58, 58, 58, 58, 58, 79, 81, 81, 58, 58, 58, 1, 9, 9, 9, 1, 11, 11, 58, 58, 58, 79, 79, 58] 81 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 25] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 229 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220508 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220508 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220508/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220508 Building REAL300000220509 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220509' /scratch/stefan/7769890/working/building/REAL300000220509 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220509 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220509/0 /scratch/stefan/7769890/working/building/REAL300000220509 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/515 `/scratch/stefan/7769890/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CN=C2C=C1) `REAL300000220509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220509 none CC1=CN2C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 1, 1, 1, 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, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [42, 42, 42, 42, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 10, 10, 3, 3, 2, 2, 2, 1, 42, 42, 42] 58 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 85 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: REAL300000220509 none CC1=CN2C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 1, 1, 1, 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, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 1, 12, 12, 42, 42, 42, 42, 42, 58, 58, 58, 42, 42, 42, 1, 1, 1, 1, 1, 2, 2, 2, 1, 12, 12, 58, 58, 42, 42, 42, 42, 1, 1, 1] 58 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 19, 20, 21, 22, 23, 36, 27, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220509 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220509 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220509/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220509 Building REAL300000220510 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220510' /scratch/stefan/7769890/working/building/REAL300000220510 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220510 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220510/0 /scratch/stefan/7769890/working/building/REAL300000220510 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/516 `/scratch/stefan/7769890/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC=CC2=CC=C(F)C=C2)N1) `REAL300000220510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220510 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC=CC2=CC=C(F)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [27, 27, 27, 27, 33, 33, 33, 27, 27, 27, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 33, 33, 7, 7, 3, 3, 1, 1, 1, 1, 27] 33 rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 79 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220510 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC=CC2=CC=C(F)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 23, 23, 27, 27, 23, 23, 27, 27, 1, 2, 2, 2, 3, 3, 11, 11, 23, 23, 27, 27, 27, 27, 1] 33 rigid atoms, others: [0, 1, 2, 3, 36, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 109 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220510 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220510 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220510/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220510 Building REAL300000220511 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220511' /scratch/stefan/7769890/working/building/REAL300000220511 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220511 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220511/0 /scratch/stefan/7769890/working/building/REAL300000220511 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/517 `/scratch/stefan/7769890/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220511 none COC1=CC=C(Br)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [63, 46, 46, 46, 46, 46, 46, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 46, 63, 63, 63, 46, 46, 12, 12, 2, 2, 2, 3, 3, 1, 46] 90 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 128 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: REAL300000220511 none COC1=CC=C(Br)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 46, 46, 46, 46, 46, 69, 82, 82, 46, 46, 46, 1, 3, 3, 3, 1, 1, 8, 8, 46, 46, 46, 69, 69, 46, 1] 90 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 22, 36, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 256 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220511 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220511 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220511/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220511 Building REAL300000220512 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220512' /scratch/stefan/7769890/working/building/REAL300000220512 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220512 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220512/0 /scratch/stefan/7769890/working/building/REAL300000220512 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/518 `/scratch/stefan/7769890/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C#N)C=C2F)N1) `REAL300000220512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) Killed Solvation calculation failed Skipping REAL300000220512 0 /scratch/stefan/7769890/working/building/REAL300000220512 /scratch/stefan/7769890/working /scratch/stefan/7769890 `0' -> `0.failed' Finished preparing REAL300000220512 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Found failed protomers Marking REAL300000220512 as failed `/scratch/stefan/7769890/working/building/REAL300000220512' -> `/scratch/stefan/7769890/failed/REAL300000220512' Building REAL300000220513 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220513' /scratch/stefan/7769890/working/building/REAL300000220513 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220513 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220513/0 /scratch/stefan/7769890/working/building/REAL300000220513 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/519 `/scratch/stefan/7769890/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC=C2Cl)N1) `REAL300000220513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220513 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 41, 41, 41, 35, 35, 35, 12, 12, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 41, 41, 12, 12, 1, 1, 35] 41 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 93 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220513 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CSC=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 11, 11, 35, 35, 1] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 83 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220513 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220513 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220513/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220513 Building REAL300000220514 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220514' /scratch/stefan/7769890/working/building/REAL300000220514 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220514 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220514/0 /scratch/stefan/7769890/working/building/REAL300000220514 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/520 `/scratch/stefan/7769890/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)CCN3C)N1) `REAL300000220514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220514 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)CCN3C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 17, 17, 28, 28, 28, 17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 28, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17] 28 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41]) total number of confs: 101 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: REAL300000220514 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)CCN3C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 3, 3, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1] 28 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 41, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 57 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220514 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220514 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220514/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220514 Building REAL300000220515 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220515' /scratch/stefan/7769890/working/building/REAL300000220515 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220515 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220515/0 /scratch/stefan/7769890/working/building/REAL300000220515 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/521 `/scratch/stefan/7769890/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)O1) `REAL300000220515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220515 none CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 12, 12, 70, 70, 70, 70, 70, 104, 138, 138, 70, 70, 70, 1, 13, 13, 13, 13, 13, 13, 1, 12, 12, 70, 70, 70, 104, 104, 70] 187 rigid atoms, others: [4, 5, 6, 7, 8, 9, 23, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 447 number of broken/clashed sets: 186 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220515 none CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 13, 13, 13, 13, 84, 84, 162, 162, 162, 162, 162, 187, 187, 187, 162, 162, 162, 13, 1, 2, 2, 2, 1, 1, 13, 84, 84, 162, 162, 162, 187, 187, 162] 187 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 455 number of broken/clashed sets: 186 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220515 none CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [162, 162, 162, 162, 70, 70, 70, 70, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 70, 162, 162, 162, 162, 162, 162, 70, 11, 11, 2, 2, 2, 3, 3, 1] 187 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 247 number of broken/clashed sets: 186 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220515 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220515 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220515/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220515 Building REAL300000220516 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220516' /scratch/stefan/7769890/working/building/REAL300000220516 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220516 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220516/0 /scratch/stefan/7769890/working/building/REAL300000220516 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/522 `/scratch/stefan/7769890/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=NC=C3)C=C2F)N1) `REAL300000220516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220516 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=NC=C3)C=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 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: [32, 32, 32, 32, 48, 58, 58, 32, 32, 32, 10, 10, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 32, 32, 32, 32, 48, 48, 10, 10, 1, 1, 3, 3, 3, 3, 1, 32] 58 rigid atoms, others: [34, 35, 40, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 41]) total number of confs: 194 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220516 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=NC=C3)C=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 32, 32, 29, 32, 41, 41, 32, 41, 41, 32, 32, 32, 1, 2, 2, 2, 3, 3, 10, 10, 32, 32, 41, 41, 41, 41, 32, 1] 58 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 41, 26] set([4, 5, 6, 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: 139 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220516 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=NC=C3)C=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 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: [41, 41, 41, 41, 58, 58, 58, 41, 41, 41, 17, 17, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 41, 41, 41, 41, 58, 58, 17, 17, 3, 3, 1, 1, 1, 1, 3, 41] 58 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 172 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220516 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220516 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220516/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220516 Building REAL300000220517 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220517' /scratch/stefan/7769890/working/building/REAL300000220517 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220517 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220517/0 /scratch/stefan/7769890/working/building/REAL300000220517 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/523 `/scratch/stefan/7769890/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=N1) `REAL300000220517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220517 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [72, 72, 72, 72, 99, 104, 104, 72, 72, 72, 12, 12, 1, 1, 1, 1, 1, 7, 7, 4, 6, 7, 7, 7, 1, 1, 72, 72, 72, 72, 99, 99, 72, 13, 12, 1, 7, 7, 7] 134 rigid atoms, others: [35, 12, 13, 14, 15, 16, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 299 number of broken/clashed sets: 133 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220517 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 13, 13, 72, 72, 72, 115, 115, 110, 115, 115, 115, 115, 72, 72, 1, 2, 2, 2, 3, 3, 1, 13, 13, 72, 115, 115, 115] 134 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 225 number of broken/clashed sets: 133 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220517 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [115, 115, 115, 115, 134, 134, 134, 115, 115, 115, 46, 46, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 115, 115, 115, 115, 134, 134, 115, 46, 46, 7, 1, 1, 1] 134 rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 307 number of broken/clashed sets: 133 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220517 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220517 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220517/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220517 Building REAL300000220518 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220518' /scratch/stefan/7769890/working/building/REAL300000220518 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220518 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220518/0 /scratch/stefan/7769890/working/building/REAL300000220518 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/524 `/scratch/stefan/7769890/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C([N+](=O)[O-])C=C2Cl)=N1) `REAL300000220518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220518 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C([N+](=O)[O-])C=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 27, 27, 27, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 15, 15, 15, 15, 27, 27, 15, 7, 7, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 103 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: REAL300000220518 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C([N+](=O)[O-])C=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 15, 15, 11, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 3, 1, 9, 9, 15, 15, 15] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 74 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220518 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220518 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220518/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220518 Building REAL300000220519 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220519' /scratch/stefan/7769890/working/building/REAL300000220519 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220519 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220519/0 /scratch/stefan/7769890/working/building/REAL300000220519 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/525 `/scratch/stefan/7769890/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC(C)C)N=C2)=N1) `REAL300000220519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220519 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC(C)C)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 63, 97, 97, 38, 38, 38, 6, 6, 1, 1, 1, 1, 1, 6, 8, 8, 1, 1, 38, 38, 38, 38, 63, 63, 38, 6, 6, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 1] 194 rigid atoms, others: [41, 12, 13, 14, 15, 16, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 367 number of broken/clashed sets: 193 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220519 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC(C)C)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 38, 38, 38, 104, 133, 133, 38, 38, 1, 2, 2, 2, 3, 3, 1, 11, 11, 38, 104, 104, 133, 133, 133, 133, 133, 133, 133, 38] 194 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 533 number of broken/clashed sets: 193 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220519 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220519 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220519/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220519 Building REAL300000220520 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220520' /scratch/stefan/7769890/working/building/REAL300000220520 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220520 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220520/0 /scratch/stefan/7769890/working/building/REAL300000220520 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/526 `/scratch/stefan/7769890/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2C2CCCCC2)=N1) `REAL300000220520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220520 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2C2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 85, 139, 164, 164, 85, 85, 85, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 85, 85, 85, 85, 139, 139, 85, 9, 9, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 546 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220520 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2C2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 85, 85, 85, 85, 85, 85, 151, 151, 151, 151, 151, 1, 2, 2, 2, 3, 3, 1, 11, 11, 85, 85, 85, 85, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 355 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220520 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2C2CCCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 151, 201, 201, 201, 151, 151, 151, 42, 42, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 201, 201, 151, 42, 42, 6, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 537 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220520 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220520 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220520/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220520 Building REAL300000220521 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220521' /scratch/stefan/7769890/working/building/REAL300000220521 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220521 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220521/0 /scratch/stefan/7769890/working/building/REAL300000220521 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/527 `/scratch/stefan/7769890/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N(C)N=C2C(F)(F)F)=N1) `REAL300000220521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220521 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N(C)N=C2C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 5, 8, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 33, 33, 33, 49, 49, 49, 33, 33, 33, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 33, 33, 33, 33, 49, 49, 33, 7, 7, 2, 2, 2] 49 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 155 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: REAL300000220521 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N(C)N=C2C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 5, 8, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 2, 2, 2, 3, 3, 1, 11, 11, 33, 33, 33] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220521 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220521 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220521/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220521 Building REAL300000220522 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220522' /scratch/stefan/7769890/working/building/REAL300000220522 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220522 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220522/0 /scratch/stefan/7769890/working/building/REAL300000220522 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/528 `/scratch/stefan/7769890/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=C2)C=C1) `REAL300000220522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220522 none COC1=CC=C(OC2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 11, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 51, 77, 77, 29, 29, 29, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 5, 5, 29, 29, 29, 51, 51, 29, 1, 1, 11, 11] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 44, 45, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 314 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220522 none COC1=CC=C(OC2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 11, 11, 11, 11, 38, 38, 143, 143, 143, 143, 143, 201, 201, 201, 143, 143, 143, 11, 11, 1, 1, 2, 2, 2, 1, 1, 11, 11, 38, 38, 143, 143, 143, 201, 201, 143, 11, 11, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 46, 47, 33, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 581 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220522 none COC1=CC=C(OC2=CC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [143, 143, 79, 143, 143, 79, 9, 9, 29, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 29, 143, 143, 143, 143, 143, 143, 143, 29, 29, 9, 9, 2, 2, 2, 3, 3, 1, 29, 29, 143, 143] 201 rigid atoms, others: [43, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 564 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220522 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220522 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220522/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220522 Building REAL300000220523 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220523' /scratch/stefan/7769890/working/building/REAL300000220523 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220523 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220523/0 /scratch/stefan/7769890/working/building/REAL300000220523 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/529 `/scratch/stefan/7769890/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(Br)=C2)=N1) `REAL300000220523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220523 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [21, 21, 21, 21, 32, 32, 32, 21, 21, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 32, 32, 21, 7, 7, 1, 1, 1] 32 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 101 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: REAL300000220523 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 7, 7, 1, 1, 1, 1, 1, 8, 8, 21, 21, 15, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 8, 8, 21, 21, 21] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 94 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220523 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220523 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220523/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220523 Building REAL300000220524 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220524' /scratch/stefan/7769890/working/building/REAL300000220524 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220524 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220524/0 /scratch/stefan/7769890/working/building/REAL300000220524 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/530 `/scratch/stefan/7769890/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220524 none CC1=CC(Cl)=CC(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 9, 9, 10, 10, 10, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 3, 3, 2, 2, 2, 1] 15 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) 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: REAL300000220524 none CC1=CC(Cl)=CC(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 15, 15, 15, 10, 10, 10, 2, 2, 2, 1, 1, 2, 2, 2, 4, 4, 15, 15, 10, 10, 10, 9] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27] set([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, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220524 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220524 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220524/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220524 Building REAL300000220525 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220525' /scratch/stefan/7769890/working/building/REAL300000220525 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220525 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220525/0 /scratch/stefan/7769890/working/building/REAL300000220525 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/531 `/scratch/stefan/7769890/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C([N+](=O)[O-])C=C2F)=N1) `REAL300000220525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220525 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C([N+](=O)[O-])C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [19, 19, 19, 19, 33, 33, 33, 19, 19, 19, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 19, 33, 33, 19, 8, 8, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 123 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220525 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C([N+](=O)[O-])C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 19, 19, 9, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 1, 9, 9, 19, 19, 19] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 96 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220525 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220525 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220525/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220525 Building REAL300000220526 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220526' /scratch/stefan/7769890/working/building/REAL300000220526 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220526 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220526/0 /scratch/stefan/7769890/working/building/REAL300000220526 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/532 `/scratch/stefan/7769890/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(C(=O)OC(C)(C)C)=C2)=N1) `REAL300000220526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220526 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(C(=O)OC(C)(C)C)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 73, 98, 98, 46, 46, 46, 6, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 11, 12, 13, 12, 1, 46, 46, 46, 46, 73, 73, 46, 6, 6, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 358 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220526 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(C(=O)OC(C)(C)C)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 46, 46, 46, 46, 46, 98, 98, 142, 143, 143, 143, 46, 1, 2, 2, 2, 3, 3, 1, 12, 12, 46, 46, 46, 143, 143, 143, 143, 143, 143, 143, 143, 143, 46] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 340 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220526 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220526 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220526/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220526 Building REAL300000220527 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220527' /scratch/stefan/7769890/working/building/REAL300000220527 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220527 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220527/0 /scratch/stefan/7769890/working/building/REAL300000220527 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/533 `/scratch/stefan/7769890/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1[N+](=O)[O-]) `REAL300000220527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220527 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 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: [44, 37, 37, 37, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 37, 37, 37, 37, 37, 37, 44, 44, 44, 37, 11, 11, 2, 2, 2, 3, 3, 1, 37, 37] 56 rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 95 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220527 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 6, 6, 37, 37, 37, 37, 37, 55, 56, 56, 37, 37, 37, 1, 1, 1, 1, 2, 2, 4, 4, 4, 1, 6, 6, 37, 37, 37, 55, 55, 37, 1, 1] 56 rigid atoms, others: [1, 2, 3, 4, 5, 38, 19, 20, 21, 22, 28, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 174 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220527 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220527 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220527/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220527 Building REAL300000220528 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220528' /scratch/stefan/7769890/working/building/REAL300000220528 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220528 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220528/0 /scratch/stefan/7769890/working/building/REAL300000220528 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/534 `/scratch/stefan/7769890/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Br)=N2)=N1) `REAL300000220528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220528 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Br)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 40, 40, 40, 32, 32, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 40, 40, 32, 9, 9, 1, 1, 1] 40 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 98 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220528 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Br)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 32, 32, 32, 32, 32, 32, 1, 2, 2, 2, 3, 3, 1, 12, 12, 32, 32, 32] 40 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 78 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220528 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220528 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220528/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220528 Building REAL300000220529 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220529' /scratch/stefan/7769890/working/building/REAL300000220529 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220529 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220529/0 /scratch/stefan/7769890/working/building/REAL300000220529 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/535 `/scratch/stefan/7769890/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN(C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220529 none CCC1=NN(C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [100, 63, 63, 63, 63, 63, 63, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 100, 100, 100, 100, 100, 63, 63, 63, 63, 11, 11, 3, 3, 2, 2, 2, 1] 116 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 301 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: REAL300000220529 none CCC1=NN(C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 63, 63, 63, 63, 63, 87, 92, 92, 63, 63, 63, 7, 7, 7, 7, 7, 2, 2, 2, 1, 11, 11, 87, 87, 63, 63, 63, 63] 116 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 275 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220529 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220529 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220529/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220529 Building REAL300000220530 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220530' /scratch/stefan/7769890/working/building/REAL300000220530 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220530 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220530/0 /scratch/stefan/7769890/working/building/REAL300000220530 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/536 `/scratch/stefan/7769890/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1OC(F)F) `REAL300000220530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220530 none CC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 22, 65, 65, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 65, 65, 108, 193, 193, 65, 65, 65, 65, 65, 65, 12, 12, 2, 2, 2, 3, 3, 1, 193] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 784 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220530 none CC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 65, 65, 65, 65, 65, 105, 142, 142, 65, 65, 65, 1, 1, 5, 35, 35, 2, 2, 2, 1, 1, 1, 9, 9, 65, 65, 65, 105, 105, 65, 35] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 580 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220530 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220530 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220530/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220530 Building REAL300000220531 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220531' /scratch/stefan/7769890/working/building/REAL300000220531 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220531 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220531/0 /scratch/stefan/7769890/working/building/REAL300000220531 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/537 `/scratch/stefan/7769890/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NN(C(F)F)C=C2)=N1) `REAL300000220531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220531 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NN(C(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 5, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [63, 62, 63, 63, 95, 104, 104, 63, 63, 63, 12, 12, 1, 1, 1, 1, 1, 12, 12, 1, 1, 62, 63, 63, 63, 95, 95, 63, 12, 12, 12, 1, 1] 120 rigid atoms, others: [32, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 353 number of broken/clashed sets: 119 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220531 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NN(C(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 5, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 63, 63, 63, 99, 99, 63, 63, 1, 2, 2, 2, 3, 3, 1, 12, 12, 99, 63, 63] 120 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 305 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220531 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220531 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220531/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220531 Building REAL300000220532 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220532' /scratch/stefan/7769890/working/building/REAL300000220532 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220532 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220532/0 /scratch/stefan/7769890/working/building/REAL300000220532 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/538 `/scratch/stefan/7769890/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC3=C(CCCC3)S2)=N1) `REAL300000220532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220532 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC3=C(CCCC3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 14, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 21, 35, 35, 35, 21, 21, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 35, 35, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1] 35 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 118 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: REAL300000220532 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC3=C(CCCC3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 14, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 60 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220532 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220532 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220532/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220532 Building REAL300000220533 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220533' /scratch/stefan/7769890/working/building/REAL300000220533 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220533 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220533/0 /scratch/stefan/7769890/working/building/REAL300000220533 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/539 `/scratch/stefan/7769890/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=CC=C2)N1) `REAL300000220533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220533 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 129, 147, 147, 83, 84, 83, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 84, 84, 84, 84, 129, 129, 12, 12, 1, 2, 2, 2, 7, 7, 1, 7, 7, 84] 153 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 474 number of broken/clashed sets: 152 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220533 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 84, 84, 84, 84, 84, 84, 130, 130, 84, 130, 130, 1, 2, 2, 2, 3, 3, 12, 12, 84, 84, 84, 84, 130, 130, 84, 130, 130, 1] 153 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 42] set([4, 5, 6, 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, 39, 40, 41]) total number of confs: 330 number of broken/clashed sets: 152 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220533 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 153, 153, 153, 130, 130, 130, 40, 40, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 153, 153, 40, 40, 7, 7, 7, 7, 1, 1, 1, 1, 1, 130] 153 rigid atoms, others: [37, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 343 number of broken/clashed sets: 152 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220533 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220533 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220533/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220533 Building REAL300000220534 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220534' /scratch/stefan/7769890/working/building/REAL300000220534 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220534 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220534/0 /scratch/stefan/7769890/working/building/REAL300000220534 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/540 `/scratch/stefan/7769890/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220534 none CC1=CC=C(F)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [31, 31, 31, 31, 31, 31, 31, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 31, 31, 31, 31, 31, 31, 11, 11, 3, 3, 2, 2, 2, 1] 39 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 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: REAL300000220534 none CC1=CC=C(F)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 39, 39, 39, 31, 31, 31, 2, 2, 2, 1, 1, 1, 7, 7, 39, 39, 31, 31, 31, 30] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 100 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220534 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220534 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220534/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220534 Building REAL300000220535 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220535' /scratch/stefan/7769890/working/building/REAL300000220535 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220535 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220535/0 /scratch/stefan/7769890/working/building/REAL300000220535 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/541 `/scratch/stefan/7769890/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CC[NH+](C)CC3)C=C2)=N1) `REAL300000220535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220535 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CC[NH+](C)CC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 9, 6, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 20, 21, 21, 31, 46, 46, 21, 21, 21, 4, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 20, 21, 21, 21, 31, 31, 21, 4, 4, 1, 1, 8, 8, 8, 9, 8, 8, 9, 8, 9, 8, 8, 1, 1] 68 rigid atoms, others: [36, 37, 49, 12, 13, 14, 15, 16, 17, 50, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220535 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CC[NH+](C)CC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 9, 6, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 21, 21, 11, 11, 60, 60, 60, 60, 60, 60, 60, 21, 21, 1, 2, 2, 2, 3, 3, 1, 11, 11, 21, 21, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 21, 21] 68 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220535 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CC[NH+](C)CC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 9, 6, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [60, 60, 60, 60, 68, 68, 68, 60, 60, 60, 16, 16, 4, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 60, 60, 60, 60, 68, 68, 60, 16, 16, 8, 8, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 8, 8] 68 rigid atoms, others: [48, 38, 39, 40, 41, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 49, 50]) total number of confs: 167 number of broken/clashed sets: 68 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220535 /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `1' /scratch/stefan/7769890/working/building/REAL300000220535/1 /scratch/stefan/7769890/working/building/REAL300000220535 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 1 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/542 `/scratch/stefan/7769890/working/3D/542' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCN(C)CC3)C=C2)=N1) `REAL300000220535.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220535/1/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: REAL300000220535 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCN(C)CC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 16, 17, 17, 27, 42, 42, 17, 17, 17, 4, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 16, 17, 17, 17, 27, 27, 17, 4, 4, 1, 1, 8, 8, 8, 9, 9, 9, 9, 8, 8, 8, 8, 1, 1] 64 rigid atoms, others: [48, 35, 36, 49, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 158 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220535 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCN(C)CC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 17, 17, 11, 11, 46, 46, 46, 46, 46, 46, 17, 17, 1, 2, 2, 2, 3, 3, 1, 11, 11, 17, 17, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 17, 17] 64 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 119 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220535 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N3CCN(C)CC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 46, 46, 46, 64, 64, 64, 46, 46, 46, 17, 17, 4, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 46, 46, 46, 46, 64, 64, 46, 17, 17, 8, 8, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 8, 8] 64 rigid atoms, others: [37, 38, 39, 40, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 48, 49]) total number of confs: 213 number of broken/clashed sets: 64 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220535 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220535 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 1: /scratch/stefan/7769890/working/building/REAL300000220535/1.* 0: /scratch/stefan/7769890/working/building/REAL300000220535/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220535 Building REAL300000220536 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220536' /scratch/stefan/7769890/working/building/REAL300000220536 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220536 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220536/0 /scratch/stefan/7769890/working/building/REAL300000220536 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/543 `/scratch/stefan/7769890/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C(C#N)C=C2)N1) `REAL300000220536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220536 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C(C#N)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 128, 146, 146, 79, 79, 79, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 1, 7, 7, 79, 79, 79, 79, 128, 128, 12, 12, 1, 2, 2, 2, 7, 7, 7, 7, 79] 150 rigid atoms, others: [35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 490 number of broken/clashed sets: 149 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220536 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C(C#N)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 79, 79, 79, 79, 79, 79, 109, 109, 79, 79, 79, 109, 109, 1, 2, 2, 2, 3, 3, 11, 11, 79, 79, 79, 79, 109, 109, 109, 109, 1] 150 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 43, 27] set([4, 5, 6, 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, 41, 42]) total number of confs: 267 number of broken/clashed sets: 149 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220536 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C(C#N)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 150, 150, 150, 109, 109, 109, 38, 38, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 150, 150, 38, 38, 7, 7, 7, 7, 1, 1, 1, 1, 109] 150 rigid atoms, others: [39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43]) total number of confs: 426 number of broken/clashed sets: 149 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220536 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220536 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220536/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220536 Building REAL300000220537 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220537' /scratch/stefan/7769890/working/building/REAL300000220537 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220537 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220537/0 /scratch/stefan/7769890/working/building/REAL300000220537 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/544 `/scratch/stefan/7769890/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C2O1) `REAL300000220537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220537 none CC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 10, 10, 3, 3, 2, 2, 2, 1, 35, 35, 35, 35] 45 rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) 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: REAL300000220537 none CC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 35, 34, 35, 35, 35, 45, 45, 45, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 45, 45, 35, 35, 35, 35, 1, 1, 1, 1] 45 rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 17, 18, 19, 20, 21, 22, 23, 38] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 121 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220537 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220537 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220537/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220537 Building REAL300000220538 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220538' /scratch/stefan/7769890/working/building/REAL300000220538 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220538 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220538/0 /scratch/stefan/7769890/working/building/REAL300000220538 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/545 `/scratch/stefan/7769890/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC3=C(CC(C)(C)CC3)S2)=N1) `REAL300000220538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220538 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC3=C(CC(C)(C)CC3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 5, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 21, 38, 38, 38, 21, 21, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 38, 38, 20, 8, 8, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1] 38 rigid atoms, others: [33, 34, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 149 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: REAL300000220538 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC3=C(CC(C)(C)CC3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 5, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 38 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 60 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220538 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220538 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220538/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220538 Building REAL300000220539 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220539' /scratch/stefan/7769890/working/building/REAL300000220539 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220539 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220539/0 /scratch/stefan/7769890/working/building/REAL300000220539 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/546 `/scratch/stefan/7769890/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C(C#N)=C2)N1) `REAL300000220539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220539 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C(C#N)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.1', 'N.1', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 24, 24, 24, 29, 29, 29, 24, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 29, 29, 7, 7, 1, 1, 1, 24] 29 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 68 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220539 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C(C#N)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.1', 'N.1', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 3, 10, 10, 24, 24, 24, 1] 29 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 71 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220539 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220539 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220539/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220539 Building REAL300000220540 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220540' /scratch/stefan/7769890/working/building/REAL300000220540 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220540 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220540/0 /scratch/stefan/7769890/working/building/REAL300000220540 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/547 `/scratch/stefan/7769890/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=CC(F)=C2)N1) `REAL300000220540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220540 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=CC(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 15, 15, 15, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 4, 4, 1, 1, 1, 9] 15 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 52 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220540 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=CC(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 6, 9, 9, 9, 1, 2, 2, 2, 3, 3, 6, 6, 9, 6, 9, 1] 15 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 53 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220540 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220540 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220540/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220540 Building REAL300000220541 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220541' /scratch/stefan/7769890/working/building/REAL300000220541 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220541 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220541/0 /scratch/stefan/7769890/working/building/REAL300000220541 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/548 `/scratch/stefan/7769890/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN(C3=CC=CC=C3)C=C2)N1) `REAL300000220541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220541 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN(C3=CC=CC=C3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 53, 53, 53, 36, 37, 36, 13, 13, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 37, 37, 37, 37, 53, 53, 13, 13, 3, 3, 1, 3, 3, 1, 1, 34] 53 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 170 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220541 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN(C3=CC=CC=C3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 2, 2, 2, 3, 3, 11, 11, 37, 37, 37, 37, 37, 37, 37, 1] 53 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220541 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN(C3=CC=CC=C3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 53, 53, 53, 37, 37, 37, 18, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 37, 37, 37, 37, 53, 53, 18, 18, 1, 1, 1, 1, 1, 3, 3, 37] 53 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 164 number of broken/clashed sets: 52 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220541 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220541 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220541/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220541 Building REAL300000220542 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220542' /scratch/stefan/7769890/working/building/REAL300000220542 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220542 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220542/0 /scratch/stefan/7769890/working/building/REAL300000220542 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/549 `/scratch/stefan/7769890/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Br) `REAL300000220542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220542 none CC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 19, 20, 20, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 2, 2, 2, 3, 3, 1, 20] 32 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 68 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: REAL300000220542 none CC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 20, 20, 20, 20, 32, 32, 32, 20, 20, 20, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 20, 20, 20, 32, 32, 20, 1] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 111 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220542 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220542 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220542/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220542 Building REAL300000220543 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220543' /scratch/stefan/7769890/working/building/REAL300000220543 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220543 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220543/0 /scratch/stefan/7769890/working/building/REAL300000220543 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/550 `/scratch/stefan/7769890/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC(Cl)=CS2)=N1) `REAL300000220543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220543 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC(Cl)=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 16, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 37, 37, 37, 21, 21, 21, 9, 9, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 37, 37, 21, 9, 9, 1] 37 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 131 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: REAL300000220543 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC(Cl)=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 16, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 11, 11, 21] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28]) total number of confs: 62 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220543 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220543 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220543/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220543 Building REAL300000220544 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220544' /scratch/stefan/7769890/working/building/REAL300000220544 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220544 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220544/0 /scratch/stefan/7769890/working/building/REAL300000220544 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/551 `/scratch/stefan/7769890/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=CC=C2Br)=N1) `REAL300000220544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220544 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [33, 33, 33, 33, 39, 39, 39, 33, 33, 33, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 39, 39, 33, 7, 7, 1, 1, 1] 39 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 83 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220544 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 33, 33, 33, 33, 33, 33, 33, 1, 2, 2, 2, 3, 3, 1, 11, 11, 33, 33, 33] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 79 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220544 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220544 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220544/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220544 Building REAL300000220545 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220545' /scratch/stefan/7769890/working/building/REAL300000220545 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220545 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220545/0 /scratch/stefan/7769890/working/building/REAL300000220545 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/552 `/scratch/stefan/7769890/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C(F)=C2)N1) `REAL300000220545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220545 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [22, 22, 22, 22, 26, 26, 26, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 26, 26, 6, 6, 1, 1, 2, 1, 22] 52 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 31, 33]) total number of confs: 59 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220545 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 9, 9, 22, 22, 44, 22, 1] 52 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 106 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220545 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220545 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220545/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220545 Building REAL300000220546 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220546' /scratch/stefan/7769890/working/building/REAL300000220546 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220546 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220546/0 /scratch/stefan/7769890/working/building/REAL300000220546 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/553 `/scratch/stefan/7769890/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(Cl)=C2)=N1) `REAL300000220546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220546 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [20, 20, 20, 20, 31, 31, 31, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 31, 31, 20, 7, 7, 1, 1, 1] 31 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 100 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: REAL300000220546 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 1, 8, 8, 20, 20, 20] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 61 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220546 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220546 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220546/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220546 Building REAL300000220547 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220547' /scratch/stefan/7769890/working/building/REAL300000220547 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220547 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220547/0 /scratch/stefan/7769890/working/building/REAL300000220547 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/554 `/scratch/stefan/7769890/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(C(F)(F)F)=C2)=N1) `REAL300000220547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220547 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 24, 24, 24, 33, 33, 33, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 24, 24, 24, 24, 33, 33, 24, 5, 5, 1, 1, 1] 33 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 94 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220547 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 24, 24, 17, 24, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 3, 1, 9, 9, 24, 24, 24] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 100 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220547 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220547 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220547/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220547 Building REAL300000220548 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220548' /scratch/stefan/7769890/working/building/REAL300000220548 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220548 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220548/0 /scratch/stefan/7769890/working/building/REAL300000220548 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/555 `/scratch/stefan/7769890/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)N=CN3C)N1) `REAL300000220548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220548 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)N=CN3C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [26, 26, 26, 26, 28, 28, 28, 26, 26, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 28, 28, 7, 7, 1, 1, 1, 1, 2, 2, 2, 26] 28 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 57 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: REAL300000220548 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)N=CN3C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 2, 2, 2, 3, 3, 11, 11, 26, 26, 26, 26, 26, 26, 26, 1] 28 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 74 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220548 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220548 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220548/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220548 Building REAL300000220549 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220549' /scratch/stefan/7769890/working/building/REAL300000220549 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220549 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220549/0 /scratch/stefan/7769890/working/building/REAL300000220549 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/556 `/scratch/stefan/7769890/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220549 none CC1=CC(Cl)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [23, 23, 23, 21, 23, 23, 23, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 23, 23, 23, 23, 23, 23, 11, 11, 3, 3, 2, 2, 2, 1] 33 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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: REAL300000220549 none CC1=CC(Cl)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 7, 7, 23, 23, 23, 23, 23, 33, 33, 33, 23, 23, 23, 2, 2, 2, 1, 1, 1, 7, 7, 33, 33, 23, 23, 23, 21] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220549 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220549 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220549/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220549 Building REAL300000220550 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220550' /scratch/stefan/7769890/working/building/REAL300000220550 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220550 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220550/0 /scratch/stefan/7769890/working/building/REAL300000220550 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/557 `/scratch/stefan/7769890/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CC3=C2OCC3)=N1) `REAL300000220550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220550 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CC3=C2OCC3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 52, 52, 52, 42, 42, 42, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 52, 52, 42, 11, 11, 1, 1, 1, 1, 1, 1] 52 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 121 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220550 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CC3=C2OCC3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 2, 2, 2, 3, 3, 1, 10, 10, 42, 42, 42, 42, 42, 42] 52 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 85 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220550 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220550 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220550/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220550 Building REAL300000220551 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220551' /scratch/stefan/7769890/working/building/REAL300000220551 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220551 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220551/0 /scratch/stefan/7769890/working/building/REAL300000220551 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/558 `/scratch/stefan/7769890/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=CC(Br)=C2)=N1) `REAL300000220551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220551 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=CC(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 29, 29, 29, 22, 22, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 29, 29, 22, 7, 7, 1, 1, 1] 29 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 77 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220551 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=CC(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 1, 9, 9, 22, 22, 22] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 66 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220551 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220551 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220551/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220551 Building REAL300000220552 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220552' /scratch/stefan/7769890/working/building/REAL300000220552 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220552 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220552/0 /scratch/stefan/7769890/working/building/REAL300000220552 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/559 `/scratch/stefan/7769890/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220552 none CCCCOC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 159, 110, 57, 22, 22, 22, 12, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 163, 163, 163, 163, 163, 163, 163, 110, 110, 22, 22, 22, 22, 7, 6, 3, 3, 2, 2, 2, 1] 201 rigid atoms, others: [45, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 689 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220552 none CCCCOC1=CC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 22, 22, 22, 22, 22, 36, 58, 58, 22, 22, 22, 47, 47, 47, 47, 47, 47, 47, 25, 25, 1, 1, 1, 1, 9, 9, 36, 36, 22, 22, 22, 22] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 409 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220552 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220552 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220552/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220552 Building REAL300000220553 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220553' /scratch/stefan/7769890/working/building/REAL300000220553 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220553 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220553/0 /scratch/stefan/7769890/working/building/REAL300000220553 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/560 `/scratch/stefan/7769890/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Br)C=CS2)=N1) `REAL300000220553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220553 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Br)C=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 17, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [34, 34, 34, 34, 39, 39, 39, 34, 34, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 39, 39, 34, 9, 9, 1, 1] 39 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 82 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: REAL300000220553 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Br)C=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 17, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 34, 34, 34, 34, 34, 1, 2, 2, 2, 3, 3, 1, 11, 11, 34, 34] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 77 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220553 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220553 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220553/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220553 Building REAL300000220554 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220554' /scratch/stefan/7769890/working/building/REAL300000220554 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220554 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220554/0 /scratch/stefan/7769890/working/building/REAL300000220554 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/561 `/scratch/stefan/7769890/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Br)=C1O) `REAL300000220554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220554 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 4, 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: [46, 37, 37, 37, 37, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 37, 37, 37, 37, 46, 46, 46, 37, 37, 10, 10, 2, 2, 2, 3, 3, 1, 74] 144 rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 177 number of broken/clashed sets: 144 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220554 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 57, 72, 72, 37, 37, 37, 1, 1, 1, 1, 4, 4, 4, 1, 1, 7, 7, 37, 37, 37, 57, 57, 37, 2] 144 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 243 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220554 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220554 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220554/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220554 Building REAL300000220555 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220555' /scratch/stefan/7769890/working/building/REAL300000220555 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220555 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220555/0 /scratch/stefan/7769890/working/building/REAL300000220555 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/562 `/scratch/stefan/7769890/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=COC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220555 none COC(=O)C1=COC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 12, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 59, 105, 59, 59, 58, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 59, 105, 105, 105, 58, 12, 12, 2, 2, 2, 3, 3, 1, 59] 119 rigid atoms, others: [34, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 268 number of broken/clashed sets: 118 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220555 none COC(=O)C1=COC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 12, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 12, 12, 59, 59, 59, 58, 58, 88, 89, 89, 59, 59, 59, 1, 12, 12, 12, 1, 12, 13, 59, 59, 59, 88, 88, 59, 1] 119 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 22, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 294 number of broken/clashed sets: 118 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220555 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220555 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220555/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220555 Building REAL300000220556 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220556' /scratch/stefan/7769890/working/building/REAL300000220556 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220556 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220556/0 /scratch/stefan/7769890/working/building/REAL300000220556 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/563 `/scratch/stefan/7769890/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(F)(F)F)C(F)=C2)=N1) `REAL300000220556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220556 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(F)(F)F)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 53, 85, 85, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 1, 1, 1, 29, 29, 29, 29, 53, 53, 29, 5, 5, 1, 1, 20, 20, 1] 201 rigid atoms, others: [35, 36, 39, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 368 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220556 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC(F)(F)F)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 29, 29, 28, 29, 83, 144, 144, 144, 144, 29, 29, 29, 1, 2, 2, 2, 3, 3, 1, 9, 9, 29, 29, 144, 144, 29] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 456 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220556 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220556 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220556/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220556 Building REAL300000220557 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220557' /scratch/stefan/7769890/working/building/REAL300000220557 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220557 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220557/0 /scratch/stefan/7769890/working/building/REAL300000220557 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/564 `/scratch/stefan/7769890/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=C(C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)OCO2) `REAL300000220557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220557 none COC1=CC2=C(C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)OCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 3, 7, 3, 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: [71, 55, 55, 55, 55, 55, 55, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 55, 55, 55, 71, 71, 71, 55, 55, 11, 11, 3, 3, 2, 2, 2, 1, 55, 55] 91 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) 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: REAL300000220557 none COC1=CC2=C(C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1)OCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 3, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 55, 55, 55, 55, 55, 81, 91, 91, 55, 55, 55, 1, 1, 1, 4, 4, 4, 1, 1, 11, 11, 81, 81, 55, 55, 55, 55, 1, 1] 91 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 39, 22, 23, 24, 38, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 282 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220557 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220557 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220557/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220557 Building REAL300000220558 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220558' /scratch/stefan/7769890/working/building/REAL300000220558 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220558 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220558/0 /scratch/stefan/7769890/working/building/REAL300000220558 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/565 `/scratch/stefan/7769890/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C(=O)[O-])=C2)N1) `REAL300000220558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220558 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C(=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 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, 31, 31, 31, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 20, 20, 20, 20, 31, 31, 6, 6, 1, 1, 1, 1, 20] 31 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 102 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: REAL300000220558 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C(=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 9, 9, 20, 20, 20, 20, 1] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 64 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220558 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220558 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220558/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220558 Building REAL300000220559 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220559' /scratch/stefan/7769890/working/building/REAL300000220559 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220559 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220559/0 /scratch/stefan/7769890/working/building/REAL300000220559 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/566 `/scratch/stefan/7769890/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(=O)[O-])=CS2)=N1) `REAL300000220559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220559 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(=O)[O-])=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [32, 32, 32, 32, 39, 39, 39, 32, 32, 32, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 39, 39, 32, 12, 12, 1, 1] 39 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 94 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: REAL300000220559 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(=O)[O-])=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 32, 32, 32, 32, 32, 32, 32, 1, 2, 2, 2, 3, 3, 1, 11, 11, 32, 32] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 77 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220559 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220559 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220559/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220559 Building REAL300000220560 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220560' /scratch/stefan/7769890/working/building/REAL300000220560 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220560 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220560/0 /scratch/stefan/7769890/working/building/REAL300000220560 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/567 `/scratch/stefan/7769890/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C([N+](=O)[O-])C(Cl)=C2)=N1) `REAL300000220560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220560 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C([N+](=O)[O-])C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [22, 22, 22, 22, 32, 32, 32, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 32, 32, 22, 6, 6, 1, 1, 1] 32 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 95 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: REAL300000220560 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C([N+](=O)[O-])C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 1, 8, 8, 22, 22, 22] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 65 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220560 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220560 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220560/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220560 Building REAL300000220561 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220561' /scratch/stefan/7769890/working/building/REAL300000220561 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220561 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220561/0 /scratch/stefan/7769890/working/building/REAL300000220561 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/568 `/scratch/stefan/7769890/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC=CC2=CC=C(F)C=C2F)=N1) `REAL300000220561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220561 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC=CC2=CC=C(F)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [63, 63, 63, 63, 103, 103, 103, 63, 63, 63, 26, 26, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 103, 103, 63, 26, 26, 11, 11, 1, 1, 1] 103 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 363 number of broken/clashed sets: 103 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220561 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC=CC2=CC=C(F)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 27, 27, 63, 63, 63, 63, 63, 63, 63, 1, 2, 2, 2, 3, 3, 1, 11, 11, 27, 27, 63, 63, 63] 103 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 152 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220561 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220561 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220561/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220561 Building REAL300000220562 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220562' /scratch/stefan/7769890/working/building/REAL300000220562 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220562 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220562/0 /scratch/stefan/7769890/working/building/REAL300000220562 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/569 `/scratch/stefan/7769890/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C2=CC=CC=C2)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220562 none COC1=CC(C2=CC=CC=C2)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 21, 21, 72, 72, 72, 72, 72, 114, 132, 132, 72, 72, 72, 7, 7, 7, 3, 1, 1, 1, 1, 1, 3, 3, 21, 21, 114, 114, 72, 72, 72, 72] 132 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 442 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: REAL300000220562 none COC1=CC(C2=CC=CC=C2)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 1, 11, 11, 40, 40, 40, 40, 40, 67, 111, 111, 40, 40, 40, 4, 4, 4, 1, 3, 3, 1, 3, 3, 1, 1, 11, 11, 67, 67, 40, 40, 40, 40] 132 rigid atoms, others: [1, 2, 3, 4, 5, 38, 11, 12, 13, 14, 37, 31] set([0, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 415 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: REAL300000220562 none COC1=CC(C2=CC=CC=C2)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [55, 40, 40, 40, 40, 40, 72, 72, 40, 72, 72, 40, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 55, 55, 55, 40, 72, 72, 40, 72, 72, 40, 40, 9, 9, 3, 3, 2, 2, 2, 1] 132 rigid atoms, others: [46, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 274 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220562 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220562 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220562/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220562 Building REAL300000220563 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220563' /scratch/stefan/7769890/working/building/REAL300000220563 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220563 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220563/0 /scratch/stefan/7769890/working/building/REAL300000220563 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/570 `/scratch/stefan/7769890/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCCC(=O)[O-]) `REAL300000220563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220563 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 21, 83, 119, 119, 150, 150, 39, 39, 39, 21, 5, 5, 2, 2, 2, 3, 3, 1, 21, 21, 119, 119, 119, 119] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 39] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 475 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220563 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 40, 72, 72, 21, 21, 21, 1, 1, 1, 1, 5, 13, 13, 25, 23, 3, 3, 3, 1, 5, 5, 21, 21, 21, 40, 40, 21, 1, 1, 13, 13, 13, 13] 201 rigid atoms, others: [1, 2, 3, 4, 5, 40, 41, 19, 20, 21, 22, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 357 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220563 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220563 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220563/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220563 Building REAL300000220564 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220564' /scratch/stefan/7769890/working/building/REAL300000220564 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220564 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220564/0 /scratch/stefan/7769890/working/building/REAL300000220564 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/571 `/scratch/stefan/7769890/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SC(F)F)C=C2)=N1) `REAL300000220564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220564 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SC(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 44, 75, 75, 25, 25, 25, 4, 4, 1, 1, 1, 1, 1, 1, 13, 51, 51, 1, 1, 25, 25, 25, 25, 44, 44, 25, 4, 4, 1, 1, 51, 1, 1] 201 rigid atoms, others: [32, 33, 35, 36, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 432 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220564 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(SC(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 25, 25, 12, 12, 104, 166, 166, 25, 25, 1, 2, 2, 2, 3, 3, 1, 12, 12, 25, 25, 166, 25, 25] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 520 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220564 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220564 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220564/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220564 Building REAL300000220565 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220565' /scratch/stefan/7769890/working/building/REAL300000220565 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220565 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220565/0 /scratch/stefan/7769890/working/building/REAL300000220565 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/572 `/scratch/stefan/7769890/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(Cl)=CC3=C2OCC3)N1) `REAL300000220565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220565 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(Cl)=CC3=C2OCC3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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, 38, 38, 38, 49, 49, 49, 38, 38, 38, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 49, 49, 12, 12, 1, 1, 1, 1, 1, 1, 38] 49 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 126 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: REAL300000220565 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(Cl)=CC3=C2OCC3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 8, 8, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 2, 2, 2, 3, 3, 8, 8, 38, 38, 38, 38, 38, 38, 1] 49 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 82 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220565 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220565 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220565/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220565 Building REAL300000220566 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220566' /scratch/stefan/7769890/working/building/REAL300000220566 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220566 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220566/0 /scratch/stefan/7769890/working/building/REAL300000220566 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/573 `/scratch/stefan/7769890/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)[O-])C=C2Cl)=N1) `REAL300000220566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220566 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)[O-])C=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 13, 13, 25, 25, 13, 5, 5, 1, 1, 1] 25 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 99 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: REAL300000220566 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)[O-])C=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 11, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 3, 3, 1, 9, 9, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 60 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220566 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220566 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220566/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220566 Building REAL300000220567 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220567' /scratch/stefan/7769890/working/building/REAL300000220567 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220567 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220567/0 /scratch/stefan/7769890/working/building/REAL300000220567 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/574 `/scratch/stefan/7769890/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CN=C3)N=N2)=N1) `REAL300000220567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220567 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CN=C3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 23, 23, 35, 49, 49, 24, 24, 24, 6, 6, 1, 1, 1, 1, 1, 8, 31, 31, 31, 31, 31, 1, 1, 24, 24, 24, 24, 35, 35, 24, 6, 6, 1, 8, 8, 31, 31, 31, 31] 201 rigid atoms, others: [34, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 217 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220567 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CN=C3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 24, 24, 24, 73, 147, 147, 147, 147, 147, 24, 23, 1, 2, 2, 2, 3, 3, 1, 12, 12, 24, 73, 73, 147, 147, 147, 147] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 398 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220567 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=CN=C3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 147, 201, 201, 201, 147, 147, 147, 42, 42, 31, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 31, 31, 147, 147, 147, 147, 201, 201, 147, 42, 42, 31, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 547 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220567 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220567 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220567/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220567 Building REAL300000220568 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220568' /scratch/stefan/7769890/working/building/REAL300000220568 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220568 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220568/0 /scratch/stefan/7769890/working/building/REAL300000220568 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/575 `/scratch/stefan/7769890/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC2=CC=CN=C12) `REAL300000220568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220568 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC2=CC=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 3, 3, 2, 2, 2, 1, 16, 16, 16, 16] 29 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 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: 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: REAL300000220568 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC2=CC=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 16, 16, 16, 16, 16, 29, 29, 29, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 29, 29, 16, 16, 16, 16, 1, 1, 1, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220568 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220568 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220568/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220568 Building REAL300000220569 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220569' /scratch/stefan/7769890/working/building/REAL300000220569 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220569 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220569/0 /scratch/stefan/7769890/working/building/REAL300000220569 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/576 `/scratch/stefan/7769890/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220569 none COC(=O)COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 92, 165, 72, 19, 19, 30, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 30, 30, 165, 165, 165, 92, 92, 30, 30, 10, 10, 2, 2, 2, 3, 3, 1, 30, 30] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42]) total number of confs: 546 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220569 none COC(=O)COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 6, 35, 4, 1, 1, 1, 1, 1, 1, 5, 5, 30, 30, 30, 30, 30, 55, 91, 91, 30, 30, 30, 1, 1, 35, 35, 35, 6, 6, 1, 1, 5, 5, 30, 30, 30, 55, 55, 30, 1, 1] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 41, 24, 25, 42, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 416 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220569 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220569 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220569/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220569 Building REAL300000220570 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220570' /scratch/stefan/7769890/working/building/REAL300000220570 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220570 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220570/0 /scratch/stefan/7769890/working/building/REAL300000220570 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/577 `/scratch/stefan/7769890/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1Cl) `REAL300000220570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220570 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 16, 16, 5, 10, 16, 16, 16, 16, 5, 5, 3, 3, 1, 1, 1, 1, 16, 16] 29 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) 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: REAL300000220570 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 5, 5, 16, 16, 16, 16, 16, 29, 29, 29, 16, 16, 16, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 29, 29, 16, 16, 16, 16, 1, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220570 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220570 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220570/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220570 Building REAL300000220571 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220571' /scratch/stefan/7769890/working/building/REAL300000220571 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220571 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220571/0 /scratch/stefan/7769890/working/building/REAL300000220571 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/578 `/scratch/stefan/7769890/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)SC(=O)N3C)N1) `REAL300000220571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220571 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)SC(=O)N3C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 27, 27, 27, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 27, 27, 6, 6, 1, 1, 1, 1, 1, 1, 22] 27 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 64 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: REAL300000220571 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)SC(=O)N3C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 9, 9, 22, 22, 22, 22, 22, 22, 1] 27 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 66 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220571 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220571 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220571/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220571 Building REAL300000220572 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220572' /scratch/stefan/7769890/working/building/REAL300000220572 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220572 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220572/0 /scratch/stefan/7769890/working/building/REAL300000220572 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/579 `/scratch/stefan/7769890/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)S2)=N1) `REAL300000220572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220572 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [32, 32, 32, 32, 39, 39, 39, 32, 32, 32, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 32, 32, 32, 32, 39, 39, 32, 12, 12, 1, 1] 39 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 101 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: REAL300000220572 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 1, 2, 2, 2, 3, 3, 1, 11, 11, 32, 32] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 75 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220572 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220572 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220572/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220572 Building REAL300000220573 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220573' /scratch/stefan/7769890/working/building/REAL300000220573 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220573 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220573/0 /scratch/stefan/7769890/working/building/REAL300000220573 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/580 `/scratch/stefan/7769890/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C(C)(C)C)N=N2)=N1) `REAL300000220573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220573 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C(C)(C)C)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 49, 65, 65, 32, 32, 32, 7, 7, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 32, 32, 32, 32, 49, 49, 32, 8, 7, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 70 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 227 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220573 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C(C)(C)C)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 32, 32, 32, 48, 48, 48, 32, 32, 1, 2, 2, 2, 3, 3, 1, 11, 11, 32, 48, 48, 48, 48, 48, 48, 48, 48, 48] 70 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220573 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220573 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220573/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220573 Building REAL300000220574 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220574' /scratch/stefan/7769890/working/building/REAL300000220574 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220574 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220574/0 /scratch/stefan/7769890/working/building/REAL300000220574 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/581 `/scratch/stefan/7769890/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)SC=C2)=N1) `REAL300000220574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220574 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)SC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 14, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [31, 31, 31, 31, 41, 41, 41, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 41, 41, 31, 9, 9, 1, 1] 41 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 109 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220574 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)SC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 14, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 1, 9, 9, 31, 31] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 73 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220574 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220574 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220574/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220574 Building REAL300000220575 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220575' /scratch/stefan/7769890/working/building/REAL300000220575 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220575 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220575/0 /scratch/stefan/7769890/working/building/REAL300000220575 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/582 `/scratch/stefan/7769890/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC(F)=C3F)O2)=N1) `REAL300000220575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220575 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC(F)=C3F)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 92, 105, 105, 61, 61, 61, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 11, 12, 12, 12, 12, 1, 60, 61, 61, 61, 92, 92, 61, 13, 12, 1, 1, 12, 12, 12] 201 rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 351 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220575 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC(F)=C3F)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 60, 60, 60, 60, 165, 165, 165, 165, 165, 165, 165, 60, 1, 2, 2, 2, 3, 3, 1, 11, 11, 61, 60, 165, 165, 165] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 258 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220575 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=CC(F)=C3F)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 201, 201, 201, 165, 165, 165, 58, 58, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 165, 165, 165, 165, 201, 201, 165, 58, 58, 12, 12, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 485 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220575 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220575 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220575/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220575 Building REAL300000220576 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220576' /scratch/stefan/7769890/working/building/REAL300000220576 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220576 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220576/0 /scratch/stefan/7769890/working/building/REAL300000220576 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/583 `/scratch/stefan/7769890/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CN1C) `REAL300000220576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220576 none COC(=O)C1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 53, 114, 53, 53, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 53, 53, 53, 114, 114, 114, 53, 13, 12, 3, 3, 2, 2, 2, 1, 53, 53, 53, 53] 139 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 289 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: REAL300000220576 none COC(=O)C1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 6, 6, 53, 53, 53, 53, 53, 82, 107, 107, 53, 53, 53, 1, 1, 1, 13, 13, 13, 1, 6, 6, 82, 82, 53, 53, 53, 53, 1, 2, 2, 2] 139 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 36, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 376 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220576 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220576 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220576/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220576 Building REAL300000220577 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220577' /scratch/stefan/7769890/working/building/REAL300000220577 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220577 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220577/0 /scratch/stefan/7769890/working/building/REAL300000220577 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/584 `/scratch/stefan/7769890/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=N1) `REAL300000220577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220577 none CCN(C)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [137, 95, 27, 95, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 27, 27, 137, 137, 137, 137, 137, 95, 95, 95, 27, 27, 9, 9, 3, 3, 2, 2, 2, 1, 27] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 475 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220577 none CCN(C)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [23, 10, 1, 10, 1, 1, 1, 1, 1, 5, 5, 27, 27, 27, 27, 27, 48, 78, 78, 27, 27, 27, 1, 1, 23, 23, 23, 23, 23, 10, 10, 10, 1, 1, 5, 5, 48, 48, 27, 27, 27, 27, 1] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 42, 22, 23] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 366 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220577 /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `1' /scratch/stefan/7769890/working/building/REAL300000220577/1 /scratch/stefan/7769890/working/building/REAL300000220577 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/585 `/scratch/stefan/7769890/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=[NH+]1) `REAL300000220577.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220577/1/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: REAL300000220577 none CCN(C)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=[NH+]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 105, 32, 105, 32, 32, 32, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 32, 32, 32, 169, 169, 169, 169, 169, 105, 105, 105, 32, 32, 10, 10, 3, 3, 2, 2, 2, 1, 32] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43]) total number of confs: 641 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: REAL300000220577 none CCN(C)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=[NH+]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 11, 1, 11, 1, 1, 1, 1, 1, 5, 5, 32, 32, 32, 32, 32, 54, 87, 87, 32, 32, 32, 1, 1, 1, 28, 28, 28, 28, 28, 11, 11, 11, 1, 1, 5, 5, 54, 54, 32, 32, 32, 32, 1] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 43, 34, 22, 23, 24] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 407 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220577 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220577 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 1: /scratch/stefan/7769890/working/building/REAL300000220577/1.* 0: /scratch/stefan/7769890/working/building/REAL300000220577/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220577 Building REAL300000220578 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220578' /scratch/stefan/7769890/working/building/REAL300000220578 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220578 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220578/0 /scratch/stefan/7769890/working/building/REAL300000220578 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/586 `/scratch/stefan/7769890/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC3=CC=C(F)C=C3S2)N1) `REAL300000220578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220578 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC3=CC=C(F)C=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 31, 31, 31, 20, 20, 20, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 21, 21, 21, 31, 31, 10, 10, 1, 1, 1, 20] 31 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 108 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: REAL300000220578 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC3=CC=C(F)C=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 11, 11, 20, 20, 20, 1] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 62 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220578 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220578 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220578/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220578 Building REAL300000220579 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220579' /scratch/stefan/7769890/working/building/REAL300000220579 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220579 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220579/0 /scratch/stefan/7769890/working/building/REAL300000220579 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/587 `/scratch/stefan/7769890/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3CC3)C=C2)=N1) `REAL300000220579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220579 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3CC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 34, 58, 58, 21, 21, 21, 3, 3, 1, 1, 1, 1, 1, 1, 6, 12, 49, 49, 1, 1, 21, 21, 21, 21, 34, 34, 21, 3, 3, 1, 1, 12, 12, 49, 49, 49, 49, 49, 1, 1] 201 rigid atoms, others: [33, 34, 42, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 331 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220579 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3CC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 21, 21, 11, 11, 63, 87, 148, 148, 21, 21, 1, 2, 2, 2, 3, 3, 1, 11, 11, 21, 21, 87, 87, 148, 148, 148, 148, 148, 21, 21] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 490 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220579 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCC3CC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 201, 201, 201, 148, 148, 148, 73, 73, 25, 25, 49, 49, 25, 10, 1, 1, 1, 1, 49, 49, 148, 148, 148, 148, 201, 201, 148, 73, 73, 49, 49, 10, 10, 1, 1, 1, 1, 1, 49, 49] 201 rigid atoms, others: [37, 38, 39, 40, 41, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43]) total number of confs: 710 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220579 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220579 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220579/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220579 Building REAL300000220580 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220580' /scratch/stefan/7769890/working/building/REAL300000220580 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220580 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220580/0 /scratch/stefan/7769890/working/building/REAL300000220580 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/588 `/scratch/stefan/7769890/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(C#N)=C2Cl)=N1) `REAL300000220580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220580 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(C#N)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.1', 'N.1', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 38, 38, 38, 32, 32, 32, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 38, 38, 32, 7, 7, 1, 1] 38 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 82 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: REAL300000220580 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(C#N)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.1', 'N.1', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 2, 2, 2, 3, 3, 1, 11, 11, 32, 32] 38 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 77 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220580 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220580 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220580/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220580 Building REAL300000220581 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220581' /scratch/stefan/7769890/working/building/REAL300000220581 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220581 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220581/0 /scratch/stefan/7769890/working/building/REAL300000220581 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/589 `/scratch/stefan/7769890/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=C(Cl)S2)=N1) `REAL300000220581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220581 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=C(Cl)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 16, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 25, 25, 25, 37, 37, 37, 25, 25, 25, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 37, 37, 25, 9, 9, 1] 37 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 116 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: REAL300000220581 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=C(Cl)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 16, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 1, 9, 9, 25] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 64 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220581 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220581 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220581/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220581 Building REAL300000220582 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220582' /scratch/stefan/7769890/working/building/REAL300000220582 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220582 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220582/0 /scratch/stefan/7769890/working/building/REAL300000220582 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/590 `/scratch/stefan/7769890/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)OC(=O)N3C)N1) `REAL300000220582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220582 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)OC(=O)N3C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 26, 26, 26, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 26, 26, 6, 6, 1, 1, 1, 2, 2, 2, 22] 26 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 63 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: REAL300000220582 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3C(=C2)OC(=O)N3C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 9, 9, 22, 22, 22, 22, 22, 22, 1] 26 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 64 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220582 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220582 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220582/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220582 Building REAL300000220583 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220583' /scratch/stefan/7769890/working/building/REAL300000220583 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220583 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220583/0 /scratch/stefan/7769890/working/building/REAL300000220583 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/591 `/scratch/stefan/7769890/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(Cl)=C2Cl)=N1) `REAL300000220583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220583 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(Cl)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [17, 17, 17, 17, 30, 30, 30, 17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 30, 30, 17, 7, 7, 1, 1] 30 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 109 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: REAL300000220583 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(Cl)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 3, 3, 1, 9, 9, 17, 17] 30 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 58 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220583 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220583 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220583/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220583 Building REAL300000220584 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220584' /scratch/stefan/7769890/working/building/REAL300000220584 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220584 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220584/0 /scratch/stefan/7769890/working/building/REAL300000220584 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/592 `/scratch/stefan/7769890/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(Cl)=C2Cl)=N1) `REAL300000220584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220584 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(Cl)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [33, 33, 33, 33, 43, 43, 43, 33, 33, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 43, 43, 33, 11, 11, 1] 43 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 114 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: REAL300000220584 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(Cl)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 33, 33, 33, 33, 33, 33, 1, 2, 2, 2, 3, 3, 1, 11, 11, 33] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 76 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220584 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220584 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220584/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220584 Building REAL300000220585 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220585' /scratch/stefan/7769890/working/building/REAL300000220585 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220585 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220585/0 /scratch/stefan/7769890/working/building/REAL300000220585 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/593 `/scratch/stefan/7769890/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC(C(F)(F)F)=C2)=N1) `REAL300000220585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220585 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 22, 22, 22, 33, 33, 33, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 22, 22, 22, 22, 33, 33, 22, 5, 5, 1, 1, 1] 33 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 104 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220585 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 1, 9, 9, 22, 22, 22] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 61 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220585 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220585 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220585/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220585 Building REAL300000220586 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220586' /scratch/stefan/7769890/working/building/REAL300000220586 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220586 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220586/0 /scratch/stefan/7769890/working/building/REAL300000220586 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/594 `/scratch/stefan/7769890/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(F)(F)F)=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220586 none CC1=CC(C(F)(F)F)=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 15, 15, 15, 15, 15, 15, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 15, 15, 15, 15, 15, 15, 9, 9, 2, 2, 2, 3, 3, 1] 27 rigid atoms, others: [38, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 84 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: REAL300000220586 none CC1=CC(C(F)(F)F)=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 27, 27, 27, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 7, 15, 15, 15, 27, 27, 15] 27 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 28, 29, 30] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 111 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220586 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220586 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220586/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220586 Building REAL300000220587 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220587' /scratch/stefan/7769890/working/building/REAL300000220587 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220587 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220587/0 /scratch/stefan/7769890/working/building/REAL300000220587 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/595 `/scratch/stefan/7769890/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCC(=O)NC3=C2)N1) `REAL300000220587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220587 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCC(=O)NC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 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: [15, 15, 15, 15, 29, 29, 29, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 29, 29, 7, 7, 1, 1, 1, 1, 1, 1, 15] 29 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 111 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220587 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCC(=O)NC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 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, 3, 6, 6, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 14, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 3, 6, 6, 15, 15, 15, 15, 15, 15, 1] 29 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 54 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220587 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220587 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220587/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220587 Building REAL300000220588 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220588' /scratch/stefan/7769890/working/building/REAL300000220588 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220588 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220588/0 /scratch/stefan/7769890/working/building/REAL300000220588 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/596 `/scratch/stefan/7769890/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2N=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)SC2=C1) `REAL300000220588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220588 none COC1=CC=C2N=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [45, 36, 35, 36, 36, 36, 36, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 36, 36, 36, 45, 45, 45, 36, 36, 11, 11, 3, 3, 2, 2, 2, 1, 36] 66 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) 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: REAL300000220588 none COC1=CC=C2N=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 35, 35, 36, 36, 36, 52, 66, 66, 36, 36, 36, 1, 1, 1, 3, 3, 3, 1, 1, 13, 13, 52, 52, 36, 36, 36, 36, 1] 66 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 38, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220588 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220588 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220588/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220588 Building REAL300000220589 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220589' /scratch/stefan/7769890/working/building/REAL300000220589 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220589 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220589/0 /scratch/stefan/7769890/working/building/REAL300000220589 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/597 `/scratch/stefan/7769890/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC=C2[N+](=O)[O-])N1) `REAL300000220589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220589 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC=C2[N+](=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 4, 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: [27, 27, 27, 27, 35, 35, 35, 27, 27, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 27, 27, 27, 27, 35, 35, 5, 5, 1, 1, 1, 27] 35 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 89 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: REAL300000220589 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC=C2[N+](=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 27, 27, 21, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 11, 11, 27, 27, 27, 1] 35 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 94 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220589 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220589 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220589/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220589 Building REAL300000220590 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220590' /scratch/stefan/7769890/working/building/REAL300000220590 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220590 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220590/0 /scratch/stefan/7769890/working/building/REAL300000220590 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/598 `/scratch/stefan/7769890/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1)=CC1=CC=CC([N+](=O)[O-])=C1) `REAL300000220590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220590 none CC(C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1)=CC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 18, 18, 68, 68, 68, 68, 68, 92, 92, 92, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 7, 7, 18, 18, 68, 68, 68, 92, 92, 68, 7, 1, 1, 1, 1] 92 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 260 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220590 none CC(C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1)=CC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [31, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 31, 31, 68, 68, 31, 68, 68, 68, 68, 68, 31, 31, 31, 12, 12, 2, 2, 2, 3, 3, 1, 31, 68, 68, 54, 68] 92 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 36] set([0, 1, 2, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 303 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220590 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220590 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220590/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220590 Building REAL300000220591 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220591' /scratch/stefan/7769890/working/building/REAL300000220591 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220591 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220591/0 /scratch/stefan/7769890/working/building/REAL300000220591 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/599 `/scratch/stefan/7769890/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC(C3=CN(C)N=C3)=CS2)=N1) `REAL300000220591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220591 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC(C3=CN(C)N=C3)=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 8, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 63, 64, 64, 94, 135, 135, 64, 64, 64, 13, 13, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 63, 64, 64, 64, 94, 94, 64, 13, 13, 13, 13, 13, 13, 13, 1] 201 rigid atoms, others: [38, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 450 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220591 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC(C3=CN(C)N=C3)=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 8, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 64, 64, 64, 172, 172, 172, 172, 172, 64, 64, 1, 2, 2, 2, 3, 3, 1, 11, 11, 172, 172, 172, 172, 172, 64] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 258 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220591 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC(C3=CN(C)N=C3)=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 8, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 172, 201, 201, 201, 172, 172, 172, 70, 70, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 172, 172, 172, 172, 201, 201, 172, 70, 70, 1, 2, 2, 2, 1, 13] 201 rigid atoms, others: [33, 37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 38]) total number of confs: 473 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220591 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220591 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220591/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220591 Building REAL300000220592 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220592' /scratch/stefan/7769890/working/building/REAL300000220592 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220592 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220592/0 /scratch/stefan/7769890/working/building/REAL300000220592 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/600 `/scratch/stefan/7769890/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(C(=O)[O-])=C2Cl)=N1) `REAL300000220592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220592 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(C(=O)[O-])=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [46, 45, 46, 46, 66, 77, 77, 46, 46, 46, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 45, 46, 46, 46, 66, 66, 46, 10, 10, 1, 1, 1] 77 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 238 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: REAL300000220592 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(C(=O)[O-])=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 46, 46, 45, 46, 46, 57, 57, 46, 46, 1, 2, 2, 2, 3, 3, 1, 12, 12, 46, 46, 45] 77 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 141 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220592 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220592 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220592/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220592 Building REAL300000220593 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220593' /scratch/stefan/7769890/working/building/REAL300000220593 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220593 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220593/0 /scratch/stefan/7769890/working/building/REAL300000220593 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/601 `/scratch/stefan/7769890/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=C(F)C=C3)N=C2)=N1) `REAL300000220593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220593 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=C(F)C=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 67, 84, 84, 41, 41, 41, 6, 6, 1, 1, 1, 1, 1, 7, 11, 11, 7, 11, 11, 11, 1, 1, 41, 41, 41, 41, 67, 67, 41, 6, 6, 1, 7, 7, 11, 11, 11, 11, 1] 201 rigid atoms, others: [35, 42, 12, 13, 14, 15, 16, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 327 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220593 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=C(F)C=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 41, 41, 41, 130, 153, 153, 130, 153, 153, 153, 41, 41, 1, 2, 2, 2, 3, 3, 1, 9, 9, 41, 130, 130, 153, 153, 153, 153, 41] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 616 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220593 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3=CC=C(F)C=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 153, 153, 153, 201, 201, 201, 153, 153, 153, 44, 44, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 153, 153, 153, 153, 201, 201, 153, 44, 44, 11, 3, 3, 1, 1, 1, 1, 11] 201 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 541 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220593 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220593 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220593/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220593 Building REAL300000220594 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220594' /scratch/stefan/7769890/working/building/REAL300000220594 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220594 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220594/0 /scratch/stefan/7769890/working/building/REAL300000220594 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/602 `/scratch/stefan/7769890/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)C=NN2C)N1) `REAL300000220594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220594 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)C=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 45, 45, 45, 33, 33, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 45, 45, 8, 8, 1, 2, 2, 2, 33] 45 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 126 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: REAL300000220594 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)C=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 33, 33, 33, 33, 33, 33, 1, 2, 2, 2, 3, 3, 10, 10, 33, 33, 33, 33, 1] 45 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 20] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 76 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220594 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220594 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220594/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220594 Building REAL300000220595 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220595' /scratch/stefan/7769890/working/building/REAL300000220595 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220595 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220595/0 /scratch/stefan/7769890/working/building/REAL300000220595 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/603 `/scratch/stefan/7769890/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220595 none CCCC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 81, 39, 39, 37, 39, 39, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 39, 139, 139, 139, 139, 139, 81, 81, 37, 39, 39, 12, 12, 3, 3, 2, 2, 2, 1, 39] 201 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 602 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: REAL300000220595 none CCCC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 39, 39, 39, 39, 39, 68, 107, 107, 39, 39, 39, 1, 11, 11, 11, 10, 10, 6, 6, 1, 1, 1, 6, 6, 68, 68, 39, 39, 39, 39, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 41, 22, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 423 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220595 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220595 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220595/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220595 Building REAL300000220596 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220596' /scratch/stefan/7769890/working/building/REAL300000220596 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220596 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220596/0 /scratch/stefan/7769890/working/building/REAL300000220596 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/604 `/scratch/stefan/7769890/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=CC(Cl)=C2)=N1) `REAL300000220596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220596 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=CC(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [25, 25, 25, 25, 33, 33, 33, 25, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 33, 33, 25, 6, 6, 1, 1, 1] 33 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 85 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220596 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=CC(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 23, 25, 25, 25, 1, 2, 2, 2, 3, 3, 1, 9, 9, 25, 23, 25] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 69 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220596 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220596 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220596/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220596 Building REAL300000220597 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220597' /scratch/stefan/7769890/working/building/REAL300000220597 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220597 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220597/0 /scratch/stefan/7769890/working/building/REAL300000220597 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/605 `/scratch/stefan/7769890/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)C1=C(Cl)C=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220597 none CCS(=O)(=O)C1=C(Cl)C=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 109, 43, 109, 109, 43, 43, 43, 25, 43, 43, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 152, 152, 152, 152, 152, 43, 43, 43, 12, 12, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [41, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 734 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220597 none CCS(=O)(=O)C1=C(Cl)C=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 43, 43, 43, 43, 43, 80, 137, 137, 43, 43, 43, 24, 24, 24, 24, 24, 1, 1, 1, 5, 5, 43, 43, 43, 80, 80, 43] 201 rigid atoms, others: [32, 33, 2, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 585 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220597 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220597 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220597/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220597 Building REAL300000220598 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220598' /scratch/stefan/7769890/working/building/REAL300000220598 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220598 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220598/0 /scratch/stefan/7769890/working/building/REAL300000220598 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/606 `/scratch/stefan/7769890/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=CC=C2SC(C)C)=N1) `REAL300000220598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220598 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=CC=C2SC(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 65, 83, 83, 37, 37, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 9, 9, 37, 37, 37, 37, 65, 65, 37, 7, 7, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 310 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220598 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=CC=C2SC(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 14, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 37, 37, 37, 37, 37, 37, 37, 111, 111, 111, 1, 2, 2, 2, 3, 3, 1, 12, 12, 37, 37, 37, 111, 111, 111, 111, 111, 111, 111] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 190 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220598 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220598 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220598/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220598 Building REAL300000220599 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220599' /scratch/stefan/7769890/working/building/REAL300000220599 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220599 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220599/0 /scratch/stefan/7769890/working/building/REAL300000220599 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/607 `/scratch/stefan/7769890/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Br)C=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220599 none COC1=C(Br)C=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [69, 57, 57, 57, 57, 57, 57, 57, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 69, 69, 69, 57, 57, 57, 11, 11, 2, 2, 2, 3, 3, 1] 85 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 85 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220599 none COC1=C(Br)C=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 57, 57, 57, 57, 57, 81, 85, 85, 57, 57, 57, 5, 5, 5, 1, 1, 1, 11, 11, 57, 57, 57, 81, 81, 57] 85 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 244 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220599 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220599 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220599/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220599 Building REAL300000220600 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220600' /scratch/stefan/7769890/working/building/REAL300000220600 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220600 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220600/0 /scratch/stefan/7769890/working/building/REAL300000220600 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/608 `/scratch/stefan/7769890/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C=C2F)=N1) `REAL300000220600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220600 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [19, 19, 19, 19, 33, 33, 33, 19, 19, 19, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 33, 33, 19, 9, 9, 1, 1, 1] 33 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 119 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220600 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 19, 19, 15, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 1, 9, 9, 19, 19, 19] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220600 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220600 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220600/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220600 Building REAL300000220601 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220601' /scratch/stefan/7769890/working/building/REAL300000220601 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220601 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220601/0 /scratch/stefan/7769890/working/building/REAL300000220601 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/609 `/scratch/stefan/7769890/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C3C(=C2)CCC(=O)N3C)=N1) `REAL300000220601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220601 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C3C(=C2)CCC(=O)N3C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 33, 33, 33, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 33, 33, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 33 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43]) total number of confs: 122 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220601 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C3C(=C2)CCC(=O)N3C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 3, 7, 7, 1, 1, 1, 1, 1, 7, 7, 19, 19, 7, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 1, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220601 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220601 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220601/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220601 Building REAL300000220602 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220602' /scratch/stefan/7769890/working/building/REAL300000220602 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220602 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220602/0 /scratch/stefan/7769890/working/building/REAL300000220602 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/610 `/scratch/stefan/7769890/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C(C(=O)[O-])=C2)N1) `REAL300000220602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220602 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C(C(=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [20, 20, 20, 20, 31, 31, 31, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 20, 20, 20, 20, 31, 31, 6, 6, 1, 1, 2, 1, 20] 62 rigid atoms, others: [32, 34, 12, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 35]) total number of confs: 104 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220602 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C(C(=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 9, 9, 20, 20, 40, 20, 1] 62 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 104 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220602 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220602 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220602/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220602 Building REAL300000220603 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220603' /scratch/stefan/7769890/working/building/REAL300000220603 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220603 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220603/0 /scratch/stefan/7769890/working/building/REAL300000220603 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/611 `/scratch/stefan/7769890/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)N=C2Cl)=N1) `REAL300000220603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220603 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)N=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 27, 27, 27, 17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 27, 27, 17, 7, 7, 1, 1] 27 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 89 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: REAL300000220603 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)N=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 17, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 3, 3, 1, 11, 11, 17, 17] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220603 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220603 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220603/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220603 Building REAL300000220604 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220604' /scratch/stefan/7769890/working/building/REAL300000220604 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220604 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220604/0 /scratch/stefan/7769890/working/building/REAL300000220604 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/612 `/scratch/stefan/7769890/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C21) `REAL300000220604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220604 none CCN1N=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [103, 59, 59, 59, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 59, 59, 59, 59, 59, 59, 103, 103, 103, 103, 103, 11, 11, 3, 3, 2, 2, 2, 1, 59, 59, 59, 59] 117 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 326 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220604 none CCN1N=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 1, 12, 12, 58, 58, 59, 59, 59, 83, 89, 89, 59, 59, 59, 1, 1, 1, 1, 1, 1, 6, 6, 6, 5, 5, 12, 12, 83, 83, 59, 59, 59, 59, 1, 1, 1, 1] 117 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 40, 41, 19, 20, 21, 22, 23, 24] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220604 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220604 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220604/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220604 Building REAL300000220605 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220605' /scratch/stefan/7769890/working/building/REAL300000220605 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220605 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220605/0 /scratch/stefan/7769890/working/building/REAL300000220605 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/613 `/scratch/stefan/7769890/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220605 none CCSC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 115, 28, 28, 28, 28, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 28, 137, 137, 137, 137, 137, 28, 28, 28, 8, 8, 3, 3, 2, 2, 2, 1, 28] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 298 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: REAL300000220605 none CCSC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 28, 28, 28, 28, 28, 49, 81, 81, 28, 28, 28, 1, 22, 22, 22, 21, 21, 1, 1, 1, 5, 5, 49, 49, 28, 28, 28, 28, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 39, 22, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 363 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220605 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220605 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220605/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220605 Building REAL300000220606 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220606' /scratch/stefan/7769890/working/building/REAL300000220606 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220606 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220606/0 /scratch/stefan/7769890/working/building/REAL300000220606 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/614 `/scratch/stefan/7769890/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=N2)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220606 none CC1=NN(C2=CC=CC=N2)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 17, 17, 39, 39, 39, 39, 39, 53, 53, 53, 39, 39, 39, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 17, 17, 53, 53, 39, 39, 39, 39] 53 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 149 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: REAL300000220606 none CC1=NN(C2=CC=CC=N2)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 53, 53, 53, 35, 35, 35, 2, 2, 2, 4, 4, 4, 4, 2, 2, 2, 7, 7, 53, 53, 35, 35, 35, 35] 53 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 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: REAL300000220606 none CC1=NN(C2=CC=CC=N2)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [35, 35, 35, 35, 35, 39, 39, 39, 39, 39, 35, 35, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 35, 35, 35, 39, 39, 39, 39, 35, 35, 35, 12, 12, 3, 3, 2, 2, 2, 1] 53 rigid atoms, others: [44, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220606 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220606 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220606/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220606 Building REAL300000220607 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220607' /scratch/stefan/7769890/working/building/REAL300000220607 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220607 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220607/0 /scratch/stefan/7769890/working/building/REAL300000220607 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/615 `/scratch/stefan/7769890/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1C#N) `REAL300000220607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220607 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [38, 29, 29, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 29, 29, 29, 29, 38, 38, 38, 29, 11, 11, 3, 3, 2, 2, 2, 1, 29, 29] 55 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 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: 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: REAL300000220607 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 48, 55, 55, 29, 29, 29, 1, 1, 1, 1, 1, 4, 4, 4, 1, 5, 5, 48, 48, 29, 29, 29, 29, 1, 1] 55 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 36, 27, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 191 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220607 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220607 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220607/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220607 Building REAL300000220608 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220608' /scratch/stefan/7769890/working/building/REAL300000220608 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220608 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220608/0 /scratch/stefan/7769890/working/building/REAL300000220608 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/616 `/scratch/stefan/7769890/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C2=CN(C)N=C2)=C1) `REAL300000220608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220608 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C2=CN(C)N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 8, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [61, 60, 61, 61, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 61, 61, 134, 134, 134, 134, 134, 61, 61, 61, 61, 61, 61, 12, 12, 3, 3, 2, 2, 2, 1, 134, 134, 134, 134, 134, 61] 191 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 39] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 234 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: REAL300000220608 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C2=CN(C)N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 8, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 61, 61, 61, 61, 61, 99, 140, 140, 61, 61, 61, 1, 1, 11, 11, 11, 11, 11, 1, 2, 2, 2, 1, 1, 9, 9, 99, 99, 61, 61, 61, 61, 11, 11, 11, 11, 11, 1] 191 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 19, 20, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 489 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: REAL300000220608 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C2=CN(C)N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 8, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 11, 42, 42, 134, 134, 134, 134, 134, 191, 191, 191, 134, 134, 134, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 42, 42, 191, 191, 134, 134, 134, 134, 1, 2, 2, 2, 1, 11] 191 rigid atoms, others: [40, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 45]) total number of confs: 560 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220608 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220608 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220608/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220608 Building REAL300000220609 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220609' /scratch/stefan/7769890/working/building/REAL300000220609 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220609 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220609/0 /scratch/stefan/7769890/working/building/REAL300000220609 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/617 `/scratch/stefan/7769890/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=C(F)C=C2)N1) `REAL300000220609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220609 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=C(F)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [76, 76, 76, 76, 118, 130, 130, 76, 76, 76, 12, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 76, 76, 76, 76, 118, 118, 12, 12, 1, 1, 6, 6, 6, 6, 76] 134 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 411 number of broken/clashed sets: 133 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220609 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=C(F)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 76, 76, 76, 76, 76, 93, 93, 76, 91, 93, 93, 1, 2, 2, 2, 3, 3, 12, 12, 76, 76, 93, 93, 93, 93, 1] 134 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 39] set([4, 5, 6, 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: 242 number of broken/clashed sets: 133 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220609 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=C(F)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [93, 93, 93, 93, 134, 134, 134, 93, 93, 93, 23, 23, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 134, 134, 23, 23, 6, 6, 1, 1, 1, 1, 93] 134 rigid atoms, others: [35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 383 number of broken/clashed sets: 133 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220609 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220609 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220609/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220609 Building REAL300000220610 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220610' /scratch/stefan/7769890/working/building/REAL300000220610 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220610 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220610/0 /scratch/stefan/7769890/working/building/REAL300000220610 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/618 `/scratch/stefan/7769890/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1N1N=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220610 none CC1=CC=CC=C1N1N=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 86, 86, 86, 86, 86, 141, 157, 157, 86, 86, 86, 8, 8, 8, 8, 2, 8, 8, 1, 1, 12, 12, 141, 141, 86, 86, 86, 86] 201 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 521 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: REAL300000220610 none CC1=CC=CC=C1N1N=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 41, 41, 141, 141, 141, 141, 141, 201, 201, 201, 141, 141, 141, 2, 2, 2, 1, 1, 1, 1, 8, 8, 41, 41, 201, 201, 141, 141, 141, 141] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 29, 30, 31] set([8, 9, 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, 39, 40, 41, 42]) total number of confs: 583 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: REAL300000220610 none CC1=CC=CC=C1N1N=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 115, 141, 141, 86, 86, 86, 86, 86, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 141, 141, 141, 141, 126, 141, 141, 86, 86, 12, 12, 3, 3, 2, 2, 2, 1] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 317 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220610 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220610 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220610/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220610 Building REAL300000220611 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220611' /scratch/stefan/7769890/working/building/REAL300000220611 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220611 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220611/0 /scratch/stefan/7769890/working/building/REAL300000220611 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/619 `/scratch/stefan/7769890/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CN(C)N=C3)S2)N1) `REAL300000220611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220611 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CN(C)N=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 75, 107, 136, 136, 75, 75, 75, 12, 12, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 75, 75, 75, 75, 107, 107, 13, 12, 1, 1, 13, 13, 13, 13, 13, 75] 191 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 421 number of broken/clashed sets: 190 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220611 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CN(C)N=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 75, 75, 75, 75, 171, 171, 171, 171, 171, 75, 1, 2, 2, 2, 3, 3, 12, 12, 75, 75, 171, 171, 171, 171, 171, 1] 191 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 265 number of broken/clashed sets: 190 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220611 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CN(C)N=C3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 171, 191, 191, 191, 170, 171, 171, 98, 98, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 171, 171, 171, 171, 191, 191, 98, 98, 13, 13, 1, 2, 2, 2, 1, 171] 191 rigid atoms, others: [34, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 39]) total number of confs: 459 number of broken/clashed sets: 190 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220611 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220611 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220611/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220611 Building REAL300000220612 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220612' /scratch/stefan/7769890/working/building/REAL300000220612 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220612 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220612/0 /scratch/stefan/7769890/working/building/REAL300000220612 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/620 `/scratch/stefan/7769890/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1)=CC1=CC=CC=C1C(F)(F)F) `REAL300000220612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220612 none CC(C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1)=CC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 13, 13, 74, 74, 74, 74, 74, 95, 95, 95, 74, 74, 74, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 13, 13, 74, 74, 74, 95, 95, 74, 5, 1, 1, 1, 1] 95 rigid atoms, others: [39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 240 number of broken/clashed sets: 94 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220612 none CC(C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1)=CC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 31, 31, 74, 74, 31, 74, 74, 74, 74, 74, 74, 31, 31, 31, 12, 12, 2, 2, 2, 3, 3, 1, 31, 74, 74, 31, 74] 95 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 37] set([0, 1, 2, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 270 number of broken/clashed sets: 94 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220612 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220612 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220612/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220612 Building REAL300000220613 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220613' /scratch/stefan/7769890/working/building/REAL300000220613 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220613 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220613/0 /scratch/stefan/7769890/working/building/REAL300000220613 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/621 `/scratch/stefan/7769890/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCN1N=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220613 none COCCCN1N=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 134, 92, 73, 27, 27, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 142, 142, 142, 134, 134, 92, 92, 73, 73, 27, 27, 9, 9, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 601 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220613 none COCCCN1N=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 19, 10, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 27, 27, 27, 27, 43, 62, 62, 27, 27, 27, 26, 26, 26, 19, 19, 10, 10, 6, 6, 1, 1, 8, 8, 27, 27, 27, 43, 43, 27] 201 rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 315 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220613 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220613 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220613/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220613 Building REAL300000220614 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220614' /scratch/stefan/7769890/working/building/REAL300000220614 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220614 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220614/0 /scratch/stefan/7769890/working/building/REAL300000220614 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/622 `/scratch/stefan/7769890/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1F) `REAL300000220614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220614 none COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [78, 57, 57, 57, 57, 57, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 57, 57, 78, 78, 78, 57, 57, 57, 12, 12, 3, 3, 2, 2, 2, 1] 99 rigid atoms, others: [36, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 151 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: REAL300000220614 none COC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 57, 57, 57, 57, 57, 79, 99, 99, 57, 57, 57, 1, 1, 4, 4, 4, 1, 1, 1, 12, 12, 79, 79, 57, 57, 57, 53] 99 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 26, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 300 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220614 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220614 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220614/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220614 Building REAL300000220615 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220615' /scratch/stefan/7769890/working/building/REAL300000220615 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220615 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220615/0 /scratch/stefan/7769890/working/building/REAL300000220615 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/623 `/scratch/stefan/7769890/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(OC)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220615 none CCC1=CC(OC)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [97, 58, 58, 58, 21, 20, 89, 58, 58, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 97, 97, 97, 97, 97, 58, 89, 89, 89, 58, 58, 12, 12, 3, 3, 2, 2, 2, 1] 166 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 478 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: REAL300000220615 none CCC1=CC(OC)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 9, 9, 58, 58, 58, 58, 58, 85, 120, 120, 58, 58, 58, 6, 6, 6, 6, 6, 1, 2, 2, 2, 1, 1, 9, 9, 85, 85, 58, 58, 58, 58] 166 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 34, 33, 29] set([0, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 394 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220615 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220615 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220615/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220615 Building REAL300000220616 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220616' /scratch/stefan/7769890/working/building/REAL300000220616 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220616 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220616/0 /scratch/stefan/7769890/working/building/REAL300000220616 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/624 `/scratch/stefan/7769890/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(F)C=CC(Br)=C2F)=N1) `REAL300000220616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220616 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(F)C=CC(Br)=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 17, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [41, 41, 41, 41, 49, 49, 49, 41, 41, 41, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 49, 49, 41, 7, 7, 1, 1] 49 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 103 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: REAL300000220616 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(F)C=CC(Br)=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 17, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 3, 3, 1, 9, 9, 41, 41] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 82 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220616 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220616 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220616/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220616 Building REAL300000220617 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220617' /scratch/stefan/7769890/working/building/REAL300000220617 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220617 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220617/0 /scratch/stefan/7769890/working/building/REAL300000220617 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/625 `/scratch/stefan/7769890/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(CCl)=C2)N1) `REAL300000220617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220617 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(CCl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [41, 41, 41, 41, 65, 99, 99, 41, 41, 41, 6, 6, 1, 1, 1, 1, 1, 1, 1, 8, 1, 41, 41, 41, 41, 65, 65, 6, 6, 1, 1, 1, 8, 8, 1, 41] 117 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 35]) total number of confs: 349 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220617 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(CCl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 41, 41, 23, 41, 41, 97, 41, 1, 2, 2, 2, 3, 3, 12, 12, 41, 41, 35, 97, 97, 41, 1] 117 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 423 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220617 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220617 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220617/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220617 Building REAL300000220618 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220618' /scratch/stefan/7769890/working/building/REAL300000220618 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220618 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220618/0 /scratch/stefan/7769890/working/building/REAL300000220618 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/626 `/scratch/stefan/7769890/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(C3CC3)N=CS2)=N1) `REAL300000220618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220618 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(C3CC3)N=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [65, 65, 65, 65, 102, 109, 109, 65, 65, 65, 10, 10, 1, 1, 1, 1, 8, 8, 1, 1, 1, 65, 65, 65, 65, 102, 102, 65, 10, 10, 8, 8, 8, 8, 8, 1] 132 rigid atoms, others: [35, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 351 number of broken/clashed sets: 131 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220618 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(C3CC3)N=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 65, 65, 102, 102, 65, 65, 65, 1, 2, 2, 2, 3, 3, 1, 12, 12, 102, 102, 102, 102, 102, 65] 132 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 253 number of broken/clashed sets: 131 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220618 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(C3CC3)N=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [102, 102, 102, 102, 132, 132, 132, 102, 102, 102, 36, 36, 8, 8, 1, 1, 1, 1, 8, 8, 8, 102, 102, 102, 102, 132, 132, 102, 36, 36, 1, 1, 1, 1, 1, 8] 132 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 346 number of broken/clashed sets: 131 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220618 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220618 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220618/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220618 Building REAL300000220619 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220619' /scratch/stefan/7769890/working/building/REAL300000220619 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220619 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220619/0 /scratch/stefan/7769890/working/building/REAL300000220619 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/627 `/scratch/stefan/7769890/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CO3)S2)N1) `REAL300000220619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220619 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CO3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [64, 64, 63, 63, 89, 98, 98, 63, 63, 63, 12, 12, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 64, 64, 64, 64, 89, 89, 13, 12, 1, 13, 13, 13, 64] 143 rigid atoms, others: [12, 13, 14, 15, 16, 17, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 294 number of broken/clashed sets: 142 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220619 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CO3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 63, 63, 63, 63, 119, 119, 119, 119, 63, 1, 2, 2, 2, 3, 3, 11, 11, 63, 119, 119, 119, 1] 143 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 200 number of broken/clashed sets: 142 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220619 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(C3=CC=CO3)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [119, 119, 119, 119, 143, 143, 143, 119, 119, 119, 74, 74, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 119, 119, 119, 119, 143, 143, 74, 74, 13, 1, 1, 1, 119] 143 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 379 number of broken/clashed sets: 142 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220619 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220619 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220619/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220619 Building REAL300000220620 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220620' /scratch/stefan/7769890/working/building/REAL300000220620 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220620 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220620/0 /scratch/stefan/7769890/working/building/REAL300000220620 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/628 `/scratch/stefan/7769890/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=C(Cl)C=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220620 none CCOC1=C(Cl)C=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', '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, 16, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [109, 90, 66, 66, 66, 66, 66, 66, 66, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 109, 109, 109, 109, 109, 66, 66, 66, 11, 11, 2, 2, 2, 3, 3, 1] 144 rigid atoms, others: [39, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 278 number of broken/clashed sets: 144 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220620 none CCOC1=C(Cl)C=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', '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, 16, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 66, 66, 66, 66, 66, 112, 132, 132, 66, 66, 66, 14, 14, 14, 14, 14, 1, 1, 1, 9, 9, 66, 66, 66, 112, 112, 66] 144 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 484 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220620 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220620 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220620/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220620 Building REAL300000220621 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220621' /scratch/stefan/7769890/working/building/REAL300000220621 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220621 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220621/0 /scratch/stefan/7769890/working/building/REAL300000220621 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/629 `/scratch/stefan/7769890/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Br)C=NN2C)=N1) `REAL300000220621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220621 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Br)C=NN2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 17, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [42, 42, 42, 42, 51, 51, 51, 42, 42, 42, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 51, 51, 42, 11, 11, 1, 2, 2, 2] 51 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 124 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: REAL300000220621 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Br)C=NN2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 17, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 42, 42, 42, 42, 42, 42, 1, 2, 2, 2, 3, 3, 1, 9, 9, 42, 42, 42, 42] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 83 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220621 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220621 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220621/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220621 Building REAL300000220622 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220622' /scratch/stefan/7769890/working/building/REAL300000220622 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220622 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220622/0 /scratch/stefan/7769890/working/building/REAL300000220622 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/630 `/scratch/stefan/7769890/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(F)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220622 none CC1=NC(F)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [21, 21, 21, 21, 21, 21, 21, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 21, 21, 21, 21, 11, 11, 3, 3, 2, 2, 2, 1] 31 rigid atoms, others: [34, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL300000220622 none CC1=NC(F)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 9, 9, 21, 21, 21, 21, 21, 31, 31, 31, 21, 21, 21, 2, 2, 2, 1, 1, 9, 9, 31, 31, 21, 21, 21, 20] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220622 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220622 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220622/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220622 Building REAL300000220623 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220623' /scratch/stefan/7769890/working/building/REAL300000220623 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220623 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220623/0 /scratch/stefan/7769890/working/building/REAL300000220623 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/631 `/scratch/stefan/7769890/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=C(C(F)(F)F)S2)=N1) `REAL300000220623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220623 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=C(C(F)(F)F)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 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: [21, 21, 21, 21, 38, 38, 38, 21, 21, 21, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 21, 21, 21, 21, 38, 38, 21, 8, 8, 1] 38 rigid atoms, others: [12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 142 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: REAL300000220623 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=C(C(F)(F)F)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 9, 9, 21] 38 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 60 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220623 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220623 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220623/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220623 Building REAL300000220624 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220624' /scratch/stefan/7769890/working/building/REAL300000220624 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220624 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220624/0 /scratch/stefan/7769890/working/building/REAL300000220624 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/632 `/scratch/stefan/7769890/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC=CC(F)=C3)C=C2)=N1) `REAL300000220624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220624 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC=CC(F)=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 21, 31, 31, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 24, 24, 24, 1, 1, 13, 13, 13, 13, 21, 21, 13, 3, 3, 1, 1, 24, 24, 24, 24, 1, 1] 201 rigid atoms, others: [36, 37, 42, 43, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 139 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220624 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC=CC(F)=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 13, 13, 58, 125, 125, 125, 125, 125, 125, 13, 13, 1, 2, 2, 2, 3, 3, 1, 9, 9, 13, 13, 125, 125, 125, 125, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 215 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220624 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC=CC(F)=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 125, 201, 201, 201, 125, 125, 125, 42, 42, 24, 14, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 125, 125, 125, 125, 201, 201, 125, 42, 42, 24, 24, 1, 1, 1, 1, 24, 24] 201 rigid atoms, others: [38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 715 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220624 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220624 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220624/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220624 Building REAL300000220625 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220625' /scratch/stefan/7769890/working/building/REAL300000220625 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220625 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220625/0 /scratch/stefan/7769890/working/building/REAL300000220625 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/633 `/scratch/stefan/7769890/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)S1) `REAL300000220625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220625 none CSC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [123, 62, 62, 62, 62, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 62, 123, 123, 123, 62, 62, 11, 11, 3, 3, 2, 2, 2, 1] 147 rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) 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: REAL300000220625 none CSC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [12, 1, 1, 1, 1, 1, 1, 11, 11, 62, 52, 62, 62, 62, 91, 110, 110, 62, 62, 62, 1, 13, 13, 13, 1, 1, 11, 11, 91, 91, 62, 62, 62, 62] 147 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 24, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220625 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220625 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220625/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220625 Building REAL300000220626 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220626' /scratch/stefan/7769890/working/building/REAL300000220626 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220626 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220626/0 /scratch/stefan/7769890/working/building/REAL300000220626 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/634 `/scratch/stefan/7769890/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Cl)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220626 none COC(=O)C1=CC=C(Cl)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 75, 175, 75, 75, 75, 75, 75, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 75, 175, 175, 175, 75, 75, 12, 12, 2, 2, 2, 3, 3, 1, 75] 201 rigid atoms, others: [37, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 407 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220626 none COC(=O)C1=CC=C(Cl)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 9, 9, 75, 75, 75, 75, 75, 111, 141, 141, 75, 75, 75, 1, 13, 13, 13, 1, 1, 9, 9, 75, 75, 75, 111, 111, 75, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 24, 38, 28, 29] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 451 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220626 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220626 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220626/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220626 Building REAL300000220627 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220627' /scratch/stefan/7769890/working/building/REAL300000220627 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220627 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220627/0 /scratch/stefan/7769890/working/building/REAL300000220627 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/635 `/scratch/stefan/7769890/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1Cl) `REAL300000220627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220627 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [15, 15, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 3, 3, 2, 2, 2, 1, 16] 29 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) 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: REAL300000220627 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 5, 5, 16, 16, 16, 16, 16, 29, 29, 29, 16, 16, 16, 1, 1, 1, 2, 2, 2, 1, 1, 5, 5, 29, 29, 16, 16, 16, 16, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220627 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220627 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220627/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220627 Building REAL300000220628 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220628' /scratch/stefan/7769890/working/building/REAL300000220628 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220628 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220628/0 /scratch/stefan/7769890/working/building/REAL300000220628 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/636 `/scratch/stefan/7769890/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1F) `REAL300000220628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220628 none CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 127, 45, 43, 45, 45, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 45, 45, 45, 161, 161, 161, 161, 161, 45, 45, 12, 12, 2, 2, 2, 3, 3, 1, 45] 201 rigid atoms, others: [38, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 419 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220628 none CCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 11, 1, 1, 1, 1, 1, 1, 6, 6, 45, 45, 45, 45, 45, 82, 123, 123, 45, 45, 45, 1, 1, 1, 36, 36, 36, 36, 36, 1, 1, 6, 6, 45, 45, 45, 82, 82, 45, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 39, 21, 22, 23, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 549 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220628 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220628 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220628/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220628 Building REAL300000220629 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220629' /scratch/stefan/7769890/working/building/REAL300000220629 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220629 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220629/0 /scratch/stefan/7769890/working/building/REAL300000220629 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/637 `/scratch/stefan/7769890/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)C3=CC=CC=C3)N=C2)=N1) `REAL300000220629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220629 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)C3=CC=CC=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 68, 106, 106, 41, 41, 41, 6, 6, 1, 1, 1, 1, 1, 1, 11, 11, 24, 24, 15, 24, 24, 1, 1, 40, 41, 41, 41, 68, 68, 41, 6, 6, 1, 1, 11, 11, 11, 24, 24, 16, 24, 24, 1] 201 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 46, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 444 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220629 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)C3=CC=CC=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 40, 40, 40, 40, 130, 130, 156, 156, 147, 156, 156, 40, 40, 1, 2, 2, 2, 3, 3, 1, 12, 12, 40, 40, 130, 130, 130, 156, 156, 149, 156, 156, 40] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 404 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220629 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)C3=CC=CC=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 156, 201, 201, 201, 156, 156, 156, 56, 56, 24, 24, 24, 24, 6, 1, 6, 1, 1, 1, 1, 1, 1, 24, 24, 156, 156, 156, 156, 201, 201, 156, 56, 56, 24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 24] 201 rigid atoms, others: [41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 549 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220629 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220629 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220629/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220629 Building REAL300000220630 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220630' /scratch/stefan/7769890/working/building/REAL300000220630 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220630 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220630/0 /scratch/stefan/7769890/working/building/REAL300000220630 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/638 `/scratch/stefan/7769890/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CCC#N)N=C2C2=CC=NC=C2)N1) `REAL300000220630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220630 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CCC#N)N=C2C2=CC=NC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.1', 'N.1', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 70, 86, 86, 38, 38, 38, 11, 11, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 1, 5, 5, 1, 5, 5, 38, 39, 39, 39, 70, 70, 11, 11, 1, 6, 6, 10, 10, 5, 5, 5, 5, 38] 201 rigid atoms, others: [36, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 369 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220630 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CCC#N)N=C2C2=CC=NC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.1', 'N.1', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 7, 7, 38, 38, 38, 100, 129, 129, 38, 38, 38, 72, 72, 38, 72, 72, 1, 2, 2, 2, 3, 3, 7, 7, 38, 100, 100, 129, 129, 72, 72, 72, 72, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 45, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 669 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220630 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CCC#N)N=C2C2=CC=NC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.1', 'N.1', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 107, 120, 120, 72, 72, 72, 23, 23, 5, 5, 5, 5, 5, 18, 32, 32, 5, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 107, 107, 23, 23, 5, 18, 18, 32, 32, 1, 1, 1, 1, 72] 201 rigid atoms, others: [41, 42, 43, 44, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45]) total number of confs: 513 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220630 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220630 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220630/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220630 Building REAL300000220631 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220631' /scratch/stefan/7769890/working/building/REAL300000220631 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220631 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220631/0 /scratch/stefan/7769890/working/building/REAL300000220631 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/639 `/scratch/stefan/7769890/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1C) `REAL300000220631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220631 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 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: [43, 28, 28, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 28, 28, 28, 28, 43, 43, 43, 28, 11, 11, 3, 3, 2, 2, 2, 1, 28, 28, 28, 28, 28] 53 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) 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: REAL300000220631 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 28, 28, 28, 28, 28, 48, 53, 53, 28, 28, 28, 1, 1, 1, 1, 4, 4, 4, 1, 5, 5, 48, 48, 28, 28, 28, 28, 1, 1, 2, 2, 2] 53 rigid atoms, others: [1, 2, 3, 4, 5, 35, 19, 20, 21, 22, 36, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220631 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220631 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220631/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220631 Building REAL300000220632 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220632' /scratch/stefan/7769890/working/building/REAL300000220632 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220632 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220632/0 /scratch/stefan/7769890/working/building/REAL300000220632 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/640 `/scratch/stefan/7769890/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=NN2C)=N1) `REAL300000220632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220632 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=NN2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [33, 33, 33, 33, 41, 41, 41, 33, 33, 33, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 41, 41, 33, 10, 10, 1, 2, 2, 2] 41 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 103 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220632 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=NN2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 33, 33, 33, 33, 33, 33, 1, 2, 2, 2, 3, 3, 1, 11, 11, 33, 33, 33, 33] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 76 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220632 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220632 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220632/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220632 Building REAL300000220633 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220633' /scratch/stefan/7769890/working/building/REAL300000220633 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220633 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220633/0 /scratch/stefan/7769890/working/building/REAL300000220633 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/641 `/scratch/stefan/7769890/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C(C)C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220633 none CC1=NN(C(C)C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [73, 72, 72, 72, 72, 147, 147, 72, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 73, 73, 73, 147, 147, 147, 147, 147, 147, 147, 72, 12, 12, 3, 3, 2, 2, 2, 1] 177 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 480 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: REAL300000220633 none CC1=NN(C(C)C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 1, 1, 1, 11, 11, 72, 72, 72, 72, 72, 115, 159, 159, 72, 72, 72, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 1, 11, 11, 115, 115, 73, 73, 73, 72] 177 rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 576 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220633 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220633 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220633/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220633 Building REAL300000220634 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220634' /scratch/stefan/7769890/working/building/REAL300000220634 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220634 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220634/0 /scratch/stefan/7769890/working/building/REAL300000220634 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/642 `/scratch/stefan/7769890/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CS2)=N1) `REAL300000220634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220634 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [34, 34, 34, 34, 40, 40, 40, 34, 34, 34, 12, 12, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 40, 40, 34, 12, 12, 1, 1] 40 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 92 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220634 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CS2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 34, 34, 34, 34, 34, 1, 2, 2, 2, 3, 3, 1, 11, 11, 34, 34] 40 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 80 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220634 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220634 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220634/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220634 Building REAL300000220635 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220635' /scratch/stefan/7769890/working/building/REAL300000220635 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220635 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220635/0 /scratch/stefan/7769890/working/building/REAL300000220635 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/643 `/scratch/stefan/7769890/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NC(Cl)=C2Cl)=N1) `REAL300000220635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220635 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NC(Cl)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 34, 34, 34, 26, 26, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 34, 34, 26, 7, 7, 1, 1] 34 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 88 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220635 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NC(Cl)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 26, 26, 26, 26, 26, 26, 26, 1, 2, 2, 2, 3, 3, 1, 9, 9, 26, 26] 34 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220635 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220635 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220635/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220635 Building REAL300000220636 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220636' /scratch/stefan/7769890/working/building/REAL300000220636 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220636 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220636/0 /scratch/stefan/7769890/working/building/REAL300000220636 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/644 `/scratch/stefan/7769890/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(F)C=CC(O)=C2F)N1) `REAL300000220636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220636 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(F)C=CC(O)=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [39, 39, 39, 39, 49, 49, 49, 39, 39, 39, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 49, 49, 11, 11, 1, 1, 2, 39] 98 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 122 number of broken/clashed sets: 96 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220636 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(F)C=CC(O)=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 38, 39, 39, 39, 39, 1, 2, 2, 2, 3, 3, 11, 11, 39, 39, 78, 1] 98 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 168 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220636 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220636 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220636/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220636 Building REAL300000220637 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220637' /scratch/stefan/7769890/working/building/REAL300000220637 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220637 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220637/0 /scratch/stefan/7769890/working/building/REAL300000220637 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/645 `/scratch/stefan/7769890/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1N1N=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220637 none COC1=CC=CC=C1N1N=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 7, 7, 4, 7, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 49, 49, 49, 49, 49, 84, 126, 126, 49, 49, 49, 17, 17, 17, 7, 6, 7, 7, 1, 1, 10, 10, 84, 84, 49, 49, 49, 49] 201 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 481 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220637 none COC1=CC=CC=C1N1N=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 33, 33, 109, 109, 109, 109, 109, 186, 201, 201, 109, 109, 109, 3, 3, 3, 1, 1, 1, 1, 7, 7, 33, 33, 186, 186, 109, 109, 109, 109] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 701 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220637 none COC1=CC=CC=C1N1N=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 109, 109, 109, 97, 109, 109, 49, 49, 49, 49, 49, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 139, 139, 139, 109, 109, 109, 109, 49, 49, 10, 10, 3, 3, 2, 2, 2, 1] 201 rigid atoms, others: [43, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 299 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220637 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220637 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220637/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220637 Building REAL300000220638 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220638' /scratch/stefan/7769890/working/building/REAL300000220638 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220638 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220638/0 /scratch/stefan/7769890/working/building/REAL300000220638 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/646 `/scratch/stefan/7769890/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OCC2CC2)=N1) `REAL300000220638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220638 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OCC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 48, 81, 81, 29, 29, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 27, 47, 47, 29, 29, 29, 29, 48, 48, 29, 8, 8, 1, 1, 1, 27, 27, 47, 47, 47, 47, 47] 201 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 433 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220638 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OCC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 29, 29, 29, 29, 83, 130, 183, 183, 1, 2, 2, 2, 3, 3, 1, 9, 9, 29, 29, 29, 130, 130, 183, 183, 183, 183, 183] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 583 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220638 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC=C2OCC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [183, 183, 183, 183, 201, 201, 201, 183, 183, 183, 90, 90, 47, 47, 47, 47, 47, 47, 47, 23, 7, 1, 1, 1, 1, 183, 183, 183, 183, 201, 201, 183, 90, 90, 47, 47, 47, 7, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 469 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220638 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220638 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220638/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220638 Building REAL300000220639 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220639' /scratch/stefan/7769890/working/building/REAL300000220639 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220639 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220639/0 /scratch/stefan/7769890/working/building/REAL300000220639 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/647 `/scratch/stefan/7769890/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1C#N) `REAL300000220639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220639 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 19, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 8, 3, 3, 1, 1, 1, 1, 19, 19] 29 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) 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: REAL300000220639 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 19, 29, 29, 29, 19, 19, 19, 1, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 29, 29, 19, 19, 19, 19, 1, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 35, 18, 19, 20, 21, 22, 36, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 96 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220639 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220639 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220639/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220639 Building REAL300000220640 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220640' /scratch/stefan/7769890/working/building/REAL300000220640 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220640 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220640/0 /scratch/stefan/7769890/working/building/REAL300000220640 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/648 `/scratch/stefan/7769890/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C(F)(F)F)S2)=N1) `REAL300000220640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220640 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C(F)(F)F)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 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: [27, 27, 27, 27, 37, 37, 37, 27, 27, 27, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 27, 27, 27, 27, 37, 37, 27, 10, 10, 1] 37 rigid atoms, others: [12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 111 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: REAL300000220640 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C(F)(F)F)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 1, 9, 9, 27] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 66 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220640 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220640 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220640/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220640 Building REAL300000220641 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220641' /scratch/stefan/7769890/working/building/REAL300000220641 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220641 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220641/0 /scratch/stefan/7769890/working/building/REAL300000220641 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/649 `/scratch/stefan/7769890/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=NC=C3C=C2)N1) `REAL300000220641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220641 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=NC=C3C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 27, 27, 27, 18, 18, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 27, 27, 5, 5, 1, 1, 1, 1, 1, 1, 18] 27 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 83 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: REAL300000220641 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=NC=C3C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 3, 8, 8, 18, 18, 18, 18, 18, 18, 1] 27 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220641 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220641 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220641/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220641 Building REAL300000220642 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220642' /scratch/stefan/7769890/working/building/REAL300000220642 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220642 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220642/0 /scratch/stefan/7769890/working/building/REAL300000220642 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/650 `/scratch/stefan/7769890/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC(Cl)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220642 none CCC1=CC=CC(Cl)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [75, 44, 44, 44, 24, 44, 44, 44, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 75, 75, 75, 75, 75, 44, 24, 44, 12, 12, 3, 3, 2, 2, 2, 1] 94 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 313 number of broken/clashed sets: 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: REAL300000220642 none CCC1=CC=CC(Cl)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 44, 44, 44, 44, 44, 65, 65, 65, 44, 44, 44, 6, 6, 6, 6, 6, 1, 1, 1, 7, 7, 65, 65, 44, 44, 44, 42] 94 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220642 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220642 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220642/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220642 Building REAL300000220643 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220643' /scratch/stefan/7769890/working/building/REAL300000220643 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220643 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220643/0 /scratch/stefan/7769890/working/building/REAL300000220643 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/651 `/scratch/stefan/7769890/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(F)F)C=C2)N1) `REAL300000220643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220643 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(F)F)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 25, 29, 29, 15, 15, 15, 3, 3, 1, 1, 1, 1, 1, 1, 12, 12, 1, 1, 15, 15, 15, 15, 25, 25, 3, 3, 1, 1, 12, 1, 1, 15] 41 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35]) total number of confs: 133 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: REAL300000220643 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(F)F)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 15, 15, 11, 11, 39, 39, 15, 15, 1, 2, 2, 2, 3, 3, 11, 11, 15, 15, 39, 15, 15, 1] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 172 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220643 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220643 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220643/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220643 Building REAL300000220644 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220644' /scratch/stefan/7769890/working/building/REAL300000220644 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220644 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220644/0 /scratch/stefan/7769890/working/building/REAL300000220644 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/652 `/scratch/stefan/7769890/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=C(C(C)(C)C)S2)=N1) `REAL300000220644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220644 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=C(C(C)(C)C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 15, 15, 15, 27, 51, 51, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 15, 15, 15, 15, 27, 27, 15, 6, 6, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 51 rigid atoms, others: [12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 216 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: REAL300000220644 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=C(C(C)(C)C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 27, 27, 27, 15, 1, 2, 2, 2, 3, 3, 1, 9, 9, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 126 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220644 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220644 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220644/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220644 Building REAL300000220645 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220645' /scratch/stefan/7769890/working/building/REAL300000220645 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220645 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220645/0 /scratch/stefan/7769890/working/building/REAL300000220645 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/653 `/scratch/stefan/7769890/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Br) `REAL300000220645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220645 none CC1=NN(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [39, 39, 39, 39, 39, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 10, 10, 2, 2, 2, 3, 3, 1] 45 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 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: REAL300000220645 none CC1=NN(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 1, 1, 1, 9, 9, 39, 39, 39, 39, 39, 45, 45, 45, 39, 39, 39, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 39, 39, 39, 45, 45, 39] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220645 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220645 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220645/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220645 Building REAL300000220646 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220646' /scratch/stefan/7769890/working/building/REAL300000220646 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220646 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220646/0 /scratch/stefan/7769890/working/building/REAL300000220646 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/654 `/scratch/stefan/7769890/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C(C)C)N1) `REAL300000220646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220646 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 98, 115, 115, 71, 71, 71, 10, 10, 1, 1, 1, 1, 1, 1, 1, 7, 7, 71, 71, 71, 71, 98, 98, 10, 10, 1, 1, 7, 7, 7, 7, 7, 7, 7, 71] 118 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 342 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220646 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 71, 71, 71, 71, 71, 102, 102, 1, 2, 2, 2, 3, 3, 12, 12, 71, 71, 102, 102, 102, 102, 102, 102, 102, 1] 118 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 290 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220646 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220646 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220646/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220646 Building REAL300000220647 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220647' /scratch/stefan/7769890/working/building/REAL300000220647 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220647 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220647/0 /scratch/stefan/7769890/working/building/REAL300000220647 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/655 `/scratch/stefan/7769890/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC=CN2C2=CC=CC=C2)N1) `REAL300000220647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220647 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC=CN2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [64, 64, 64, 64, 99, 105, 105, 64, 64, 64, 9, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 64, 65, 65, 65, 99, 99, 9, 9, 1, 1, 6, 6, 1, 6, 6, 64] 113 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 333 number of broken/clashed sets: 112 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220647 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC=CN2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 64, 64, 64, 64, 64, 82, 82, 64, 82, 82, 1, 2, 2, 2, 3, 3, 12, 12, 64, 64, 82, 82, 66, 82, 82, 1] 113 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 206 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220647 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC=CN2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [82, 82, 82, 82, 113, 113, 113, 82, 82, 82, 21, 21, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 113, 113, 21, 21, 6, 6, 1, 1, 1, 1, 1, 82] 113 rigid atoms, others: [34, 35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 311 number of broken/clashed sets: 112 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220647 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220647 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220647/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220647 Building REAL300000220648 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220648' /scratch/stefan/7769890/working/building/REAL300000220648 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220648 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220648/0 /scratch/stefan/7769890/working/building/REAL300000220648 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/656 `/scratch/stefan/7769890/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N=CS1) `REAL300000220648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220648 none CCOC(=O)C1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [143, 120, 114, 50, 114, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 50, 50, 50, 143, 143, 143, 143, 143, 11, 11, 2, 2, 2, 3, 3, 1, 50] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 413 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220648 none CCOC(=O)C1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 13, 9, 1, 9, 1, 1, 1, 10, 10, 49, 49, 50, 50, 50, 82, 106, 106, 50, 50, 50, 1, 1, 1, 31, 31, 31, 31, 31, 10, 10, 50, 50, 50, 82, 82, 50, 1] 201 rigid atoms, others: [3, 5, 6, 7, 21, 22, 23, 37] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 468 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220648 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220648 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220648/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220648 Building REAL300000220649 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220649' /scratch/stefan/7769890/working/building/REAL300000220649 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220649 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220649/0 /scratch/stefan/7769890/working/building/REAL300000220649 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/657 `/scratch/stefan/7769890/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CN(C)N=C3)C=C2)N1) `REAL300000220649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220649 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CN(C)N=C3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 21, 28, 28, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 11, 11, 11, 11, 21, 21, 4, 4, 1, 1, 5, 5, 5, 5, 5, 1, 1, 11] 45 rigid atoms, others: [33, 34, 40, 41, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 42]) total number of confs: 112 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220649 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CN(C)N=C3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 8, 8, 11, 11, 8, 8, 25, 25, 25, 25, 25, 11, 11, 1, 2, 2, 2, 3, 3, 8, 8, 11, 11, 25, 25, 25, 25, 25, 11, 11, 1] 45 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 42] set([4, 5, 6, 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, 39, 40, 41]) total number of confs: 77 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220649 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CN(C)N=C3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 45, 45, 45, 25, 25, 25, 11, 11, 2, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 25, 25, 25, 25, 45, 45, 11, 11, 5, 5, 1, 2, 2, 2, 1, 5, 5, 25] 45 rigid atoms, others: [35, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 40, 41, 42]) total number of confs: 181 number of broken/clashed sets: 45 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220649 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220649 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220649/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220649 Building REAL300000220650 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220650' /scratch/stefan/7769890/working/building/REAL300000220650 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220650 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220650/0 /scratch/stefan/7769890/working/building/REAL300000220650 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/658 `/scratch/stefan/7769890/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)C=C2N2C=NC=N2)N1) `REAL300000220650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220650 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)C=C2N2C=NC=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 95, 124, 124, 54, 54, 54, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 54, 54, 54, 54, 95, 95, 9, 9, 1, 1, 1, 10, 10, 54] 146 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 439 number of broken/clashed sets: 145 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220650 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)C=C2N2C=NC=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 54, 54, 36, 54, 54, 54, 54, 103, 103, 103, 103, 1, 2, 2, 2, 3, 3, 12, 12, 54, 54, 54, 103, 103, 1] 146 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 25] set([4, 5, 6, 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: 258 number of broken/clashed sets: 145 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220650 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)C=C2N2C=NC=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 146, 146, 146, 103, 103, 103, 35, 35, 10, 10, 10, 1, 10, 10, 10, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 146, 146, 35, 35, 10, 10, 10, 1, 1, 103] 146 rigid atoms, others: [36, 37, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 450 number of broken/clashed sets: 145 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220650 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220650 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220650/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220650 Building REAL300000220651 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220651' /scratch/stefan/7769890/working/building/REAL300000220651 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220651 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220651/0 /scratch/stefan/7769890/working/building/REAL300000220651 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/659 `/scratch/stefan/7769890/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220651 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 3, 3, 2, 2, 2, 1] 42 rigid atoms, others: [40, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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: REAL300000220651 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 34, 34, 34, 34, 34, 42, 42, 42, 34, 34, 34, 2, 2, 2, 1, 2, 2, 2, 1, 9, 9, 42, 42, 34, 34, 34, 33] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 9, 10, 11, 28] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220651 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220651 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220651/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220651 Building REAL300000220652 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220652' /scratch/stefan/7769890/working/building/REAL300000220652 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220652 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220652/0 /scratch/stefan/7769890/working/building/REAL300000220652 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/660 `/scratch/stefan/7769890/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(F)C=CC=C2Br)=N1) `REAL300000220652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220652 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(F)C=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [35, 35, 35, 35, 43, 43, 43, 35, 35, 35, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 43, 43, 35, 9, 9, 1, 1, 1] 43 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 101 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: REAL300000220652 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(F)C=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 35, 35, 35, 12, 35, 35, 35, 1, 2, 2, 2, 3, 3, 1, 12, 12, 35, 22, 35] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 136 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220652 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220652 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220652/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220652 Building REAL300000220653 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220653' /scratch/stefan/7769890/working/building/REAL300000220653 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220653 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220653/0 /scratch/stefan/7769890/working/building/REAL300000220653 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/661 `/scratch/stefan/7769890/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C([N+](=O)[O-])C=N2)=N1) `REAL300000220653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220653 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C([N+](=O)[O-])C=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [19, 19, 19, 19, 31, 31, 31, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 19, 19, 31, 31, 19, 6, 6, 1, 1, 1] 31 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 106 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: REAL300000220653 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C([N+](=O)[O-])C=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 1, 9, 9, 19, 19, 19] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 58 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220653 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220653 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220653/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220653 Building REAL300000220654 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220654' /scratch/stefan/7769890/working/building/REAL300000220654 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220654 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220654/0 /scratch/stefan/7769890/working/building/REAL300000220654 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/662 `/scratch/stefan/7769890/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)C)C=C2C(F)(F)F)=N1) `REAL300000220654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220654 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)C)C=C2C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 57, 71, 71, 32, 32, 32, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 2, 2, 2, 32, 32, 32, 32, 57, 57, 32, 5, 5, 1, 1, 6, 6, 6, 6, 6, 6, 1] 71 rigid atoms, others: [35, 36, 43, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 276 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220654 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)C)C=C2C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 32, 32, 23, 28, 60, 60, 32, 32, 32, 32, 32, 32, 1, 2, 2, 2, 3, 3, 1, 12, 12, 32, 32, 60, 60, 60, 60, 60, 60, 32] 71 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 221 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220654 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220654 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220654/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220654 Building REAL300000220655 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220655' /scratch/stefan/7769890/working/building/REAL300000220655 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220655 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220655/0 /scratch/stefan/7769890/working/building/REAL300000220655 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/663 `/scratch/stefan/7769890/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=CC=C2)N1) `REAL300000220655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220655 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 115, 131, 131, 66, 66, 66, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 66, 66, 66, 66, 115, 115, 11, 11, 1, 1, 7, 7, 1, 7, 7, 66] 140 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 460 number of broken/clashed sets: 139 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220655 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 66, 66, 66, 66, 66, 91, 91, 66, 91, 91, 1, 2, 2, 2, 3, 3, 11, 11, 66, 66, 91, 91, 87, 91, 91, 1] 140 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 276 number of broken/clashed sets: 139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220655 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [91, 91, 91, 91, 140, 140, 140, 91, 91, 91, 25, 25, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 140, 140, 25, 25, 7, 7, 1, 1, 1, 1, 1, 91] 140 rigid atoms, others: [34, 35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 431 number of broken/clashed sets: 139 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220655 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220655 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220655/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220655 Building REAL300000220656 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220656' /scratch/stefan/7769890/working/building/REAL300000220656 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220656 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220656/0 /scratch/stefan/7769890/working/building/REAL300000220656 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/664 `/scratch/stefan/7769890/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC(F)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220656 none CCC1=CC=CC(F)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [75, 45, 45, 45, 22, 45, 45, 45, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 75, 75, 75, 75, 75, 45, 44, 45, 11, 11, 3, 3, 2, 2, 2, 1] 95 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 352 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220656 none CCC1=CC=CC(F)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 45, 45, 45, 45, 45, 67, 77, 77, 45, 45, 45, 6, 6, 6, 6, 6, 1, 1, 1, 9, 9, 67, 67, 45, 45, 45, 43] 95 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220656 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220656 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220656/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220656 Building REAL300000220657 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220657' /scratch/stefan/7769890/working/building/REAL300000220657 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220657 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220657/0 /scratch/stefan/7769890/working/building/REAL300000220657 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/665 `/scratch/stefan/7769890/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)C=CS2)N1) `REAL300000220657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220657 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)C=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [29, 29, 29, 29, 41, 41, 41, 29, 29, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 41, 41, 9, 9, 1, 1, 29] 41 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 118 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220657 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(Cl)C=CS2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 29, 29, 29, 29, 29, 1, 2, 2, 2, 3, 3, 11, 11, 29, 29, 1] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 76 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220657 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220657 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220657/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220657 Building REAL300000220658 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220658' /scratch/stefan/7769890/working/building/REAL300000220658 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220658 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220658/0 /scratch/stefan/7769890/working/building/REAL300000220658 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/666 `/scratch/stefan/7769890/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)C(C)C)N=C2)=N1) `REAL300000220658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220658 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)C(C)C)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 69, 96, 96, 40, 40, 40, 5, 5, 1, 1, 1, 1, 1, 1, 12, 12, 17, 17, 1, 1, 40, 40, 40, 40, 69, 69, 40, 5, 5, 1, 1, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 1] 201 rigid atoms, others: [33, 34, 45, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 384 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220658 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)C(C)C)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 40, 40, 40, 40, 140, 140, 157, 157, 40, 40, 1, 2, 2, 2, 3, 3, 1, 11, 11, 40, 40, 140, 140, 140, 157, 157, 157, 157, 157, 157, 157, 40] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 450 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220658 /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `1' /scratch/stefan/7769890/working/building/REAL300000220658/1 /scratch/stefan/7769890/working/building/REAL300000220658 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/667 `/scratch/stefan/7769890/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)C(C)C)[NH+]=C2)=N1) `REAL300000220658.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220658/1/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: REAL300000220658 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)C(C)C)[NH+]=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 6, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 66, 104, 104, 41, 41, 41, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 23, 23, 1, 1, 1, 41, 41, 41, 41, 66, 66, 41, 5, 5, 1, 1, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 1] 201 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 46, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 424 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220658 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)C(C)C)[NH+]=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 6, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 41, 41, 41, 41, 157, 157, 172, 172, 41, 41, 41, 1, 2, 2, 2, 3, 3, 1, 11, 11, 41, 41, 157, 157, 157, 172, 172, 172, 172, 172, 172, 172, 41] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 475 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220658 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220658 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 1: /scratch/stefan/7769890/working/building/REAL300000220658/1.* 0: /scratch/stefan/7769890/working/building/REAL300000220658/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220658 Building REAL300000220659 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220659' /scratch/stefan/7769890/working/building/REAL300000220659 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220659 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220659/0 /scratch/stefan/7769890/working/building/REAL300000220659 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/668 `/scratch/stefan/7769890/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C([N+](=O)[O-])C=C2[N+](=O)[O-])=N1) `REAL300000220659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220659 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C([N+](=O)[O-])C=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 35, 35, 35, 27, 27, 27, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 27, 27, 27, 27, 35, 35, 27, 5, 5, 1, 1, 1] 35 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 93 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: REAL300000220659 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C([N+](=O)[O-])C=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 27, 27, 11, 11, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 1, 11, 11, 27, 27, 27] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 165 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220659 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220659 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220659/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220659 Building REAL300000220660 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220660' /scratch/stefan/7769890/working/building/REAL300000220660 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220660 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220660/0 /scratch/stefan/7769890/working/building/REAL300000220660 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/669 `/scratch/stefan/7769890/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C(Cl)=C2)=N1) `REAL300000220660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220660 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [21, 21, 21, 21, 32, 32, 32, 21, 21, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 32, 32, 21, 7, 7, 1, 1, 1] 32 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 101 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: REAL300000220660 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 7, 7, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 8, 8, 21, 21, 21] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 64 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220660 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220660 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220660/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220660 Building REAL300000220661 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220661' /scratch/stefan/7769890/working/building/REAL300000220661 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220661 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220661/0 /scratch/stefan/7769890/working/building/REAL300000220661 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/670 `/scratch/stefan/7769890/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=N1) `REAL300000220661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220661 none COCCN(C)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 130, 85, 50, 26, 50, 26, 26, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 26, 26, 146, 146, 146, 130, 130, 85, 85, 50, 50, 50, 26, 26, 9, 9, 2, 2, 2, 3, 3, 1, 26] 201 rigid atoms, others: [45, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46]) total number of confs: 670 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220661 none COCCN(C)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 7, 5, 1, 5, 1, 1, 1, 1, 1, 5, 5, 26, 26, 26, 26, 26, 45, 71, 71, 26, 26, 26, 1, 1, 19, 19, 19, 11, 11, 7, 7, 5, 5, 5, 1, 1, 5, 5, 26, 26, 26, 45, 45, 26, 1] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 46, 24, 25, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 314 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220661 /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `1' /scratch/stefan/7769890/working/building/REAL300000220661/1 /scratch/stefan/7769890/working/building/REAL300000220661 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/671 `/scratch/stefan/7769890/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=[NH+]1) `REAL300000220661.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220661/1/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: REAL300000220661 none COCCN(C)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=[NH+]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 178, 126, 68, 22, 68, 22, 22, 22, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 22, 22, 22, 188, 188, 188, 178, 178, 126, 126, 68, 68, 68, 22, 22, 11, 11, 2, 2, 2, 3, 3, 1, 22] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47]) total number of confs: 772 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220661 none COCCN(C)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=[NH+]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 19, 7, 1, 7, 1, 1, 1, 1, 1, 5, 5, 22, 22, 22, 22, 22, 30, 44, 44, 22, 22, 22, 1, 1, 1, 67, 67, 67, 35, 35, 19, 19, 7, 7, 7, 1, 1, 5, 5, 22, 22, 22, 30, 30, 22, 1] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 47, 24, 25, 26, 38] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 342 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220661 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220661 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 1: /scratch/stefan/7769890/working/building/REAL300000220661/1.* 0: /scratch/stefan/7769890/working/building/REAL300000220661/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220661 Building REAL300000220662 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220662' /scratch/stefan/7769890/working/building/REAL300000220662 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220662 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220662/0 /scratch/stefan/7769890/working/building/REAL300000220662 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/672 `/scratch/stefan/7769890/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(C)C(=O)[O-])C=C2)=N1) `REAL300000220662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220662 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(C)C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 39, 67, 67, 21, 21, 21, 3, 3, 1, 1, 1, 1, 1, 1, 9, 23, 23, 34, 34, 1, 1, 21, 21, 21, 21, 39, 39, 21, 3, 3, 1, 1, 23, 23, 23, 23, 1, 1] 201 rigid atoms, others: [34, 35, 40, 41, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 358 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220662 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(C)C(=O)[O-])C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 21, 21, 12, 12, 78, 132, 132, 167, 167, 21, 21, 1, 2, 2, 2, 3, 3, 1, 12, 12, 21, 21, 132, 132, 132, 132, 21, 21] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 582 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220662 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220662 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220662/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220662 Building REAL300000220663 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220663' /scratch/stefan/7769890/working/building/REAL300000220663 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220663 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220663/0 /scratch/stefan/7769890/working/building/REAL300000220663 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/673 `/scratch/stefan/7769890/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N=C3C=C(Cl)C=CN32)=N1) `REAL300000220663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220663 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N=C3C=C(Cl)C=CN32)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 16, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 45, 45, 45, 55, 55, 55, 45, 45, 45, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 55, 55, 45, 11, 11, 1, 1, 1] 55 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 125 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220663 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N=C3C=C(Cl)C=CN32)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 16, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 2, 2, 2, 3, 3, 1, 11, 11, 45, 45, 45] 55 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220663 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220663 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220663/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220663 Building REAL300000220664 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220664' /scratch/stefan/7769890/working/building/REAL300000220664 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220664 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220664/0 /scratch/stefan/7769890/working/building/REAL300000220664 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/674 `/scratch/stefan/7769890/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C(C)(C)C)N=C2)=N1) `REAL300000220664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220664 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C(C)(C)C)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 13, 25, 25, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 13, 13, 13, 13, 13, 13, 13, 3, 3, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1] 25 rigid atoms, others: [32, 42, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 76 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: REAL300000220664 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C(C)(C)C)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 9, 9, 25, 25, 25, 13, 13, 1, 2, 2, 2, 3, 3, 1, 9, 9, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 134 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220664 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220664 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220664/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220664 Building REAL300000220665 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220665' /scratch/stefan/7769890/working/building/REAL300000220665 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220665 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220665/0 /scratch/stefan/7769890/working/building/REAL300000220665 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/675 `/scratch/stefan/7769890/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C(C)C)N=N2)=N1) `REAL300000220665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220665 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C(C)C)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 8, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 75, 75, 104, 121, 121, 76, 76, 76, 12, 12, 1, 1, 1, 1, 1, 13, 13, 1, 1, 76, 76, 76, 76, 104, 104, 76, 12, 12, 1, 13, 13, 13, 13, 13, 13, 13] 145 rigid atoms, others: [12, 13, 14, 15, 16, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 382 number of broken/clashed sets: 144 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220665 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C(C)C)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 8, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 76, 76, 76, 123, 123, 76, 75, 1, 2, 2, 2, 3, 3, 1, 12, 12, 76, 123, 123, 123, 123, 123, 123, 123] 145 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 350 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220665 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220665 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220665/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220665 Building REAL300000220666 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220666' /scratch/stefan/7769890/working/building/REAL300000220666 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220666 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220666/0 /scratch/stefan/7769890/working/building/REAL300000220666 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/676 `/scratch/stefan/7769890/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(S(N)(=O)=O)=C2)=N1) `REAL300000220666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220666 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(S(N)(=O)=O)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [29, 29, 29, 29, 46, 54, 54, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 29, 29, 29, 29, 46, 46, 29, 5, 5, 1, 1, 5, 5, 1] 129 rigid atoms, others: [33, 34, 37, 12, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 188 number of broken/clashed sets: 129 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220666 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(S(N)(=O)=O)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 29, 29, 27, 27, 29, 29, 91, 91, 91, 29, 1, 2, 2, 2, 3, 3, 1, 9, 9, 29, 29, 91, 91, 29] 129 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 342 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220666 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220666 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220666/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220666 Building REAL300000220667 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220667' /scratch/stefan/7769890/working/building/REAL300000220667 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220667 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220667/0 /scratch/stefan/7769890/working/building/REAL300000220667 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/677 `/scratch/stefan/7769890/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC=CC2=CC=C(F)C(F)=C2)=N1) `REAL300000220667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220667 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC=CC2=CC=C(F)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 53, 53, 53, 76, 76, 76, 53, 53, 53, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 76, 76, 53, 11, 11, 5, 5, 1, 1, 1] 76 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 221 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220667 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC=CC2=CC=C(F)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 22, 22, 53, 53, 53, 53, 53, 53, 53, 1, 2, 2, 2, 3, 3, 1, 10, 10, 22, 22, 53, 53, 53] 76 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220667 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220667 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220667/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220667 Building REAL300000220668 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220668' /scratch/stefan/7769890/working/building/REAL300000220668 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220668 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220668/0 /scratch/stefan/7769890/working/building/REAL300000220668 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/678 `/scratch/stefan/7769890/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Br)=C1) `REAL300000220668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220668 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [43, 21, 12, 31, 31, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 31, 31, 31, 43, 43, 43, 31, 31, 12, 12, 2, 2, 2, 3, 3, 1, 31] 61 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 171 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220668 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [2, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 43, 61, 61, 31, 31, 31, 1, 1, 1, 3, 3, 3, 1, 1, 7, 7, 31, 31, 31, 43, 43, 31, 1] 61 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 197 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220668 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220668 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220668/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220668 Building REAL300000220669 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220669' /scratch/stefan/7769890/working/building/REAL300000220669 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220669 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220669/0 /scratch/stefan/7769890/working/building/REAL300000220669 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/679 `/scratch/stefan/7769890/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=N2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220669 none CC1=NN(C2=CC=CC=N2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 21, 21, 55, 55, 55, 55, 55, 63, 63, 63, 55, 55, 55, 4, 4, 4, 1, 1, 1, 1, 21, 21, 55, 55, 55, 63, 63, 55] 63 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 135 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220669 none CC1=NN(C2=CC=CC=N2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 11, 11, 49, 49, 49, 49, 49, 63, 63, 63, 49, 49, 49, 2, 2, 2, 4, 4, 4, 4, 11, 11, 49, 49, 49, 63, 63, 49] 63 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 161 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220669 none CC1=NN(C2=CC=CC=N2)C(Cl)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [49, 49, 49, 49, 49, 55, 55, 55, 55, 55, 49, 49, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 49, 49, 49, 55, 55, 55, 55, 12, 12, 2, 2, 2, 3, 3, 1] 63 rigid atoms, others: [41, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 62 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220669 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220669 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220669/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220669 Building REAL300000220670 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220670' /scratch/stefan/7769890/working/building/REAL300000220670 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220670 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220670/0 /scratch/stefan/7769890/working/building/REAL300000220670 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/680 `/scratch/stefan/7769890/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=C(C[NH+](C)C)S2)=N1) `REAL300000220670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220670 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=C(C[NH+](C)C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'S.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 5, 9, 6, 5, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [62, 62, 62, 62, 92, 121, 121, 62, 62, 62, 13, 13, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 62, 62, 62, 62, 92, 92, 62, 13, 13, 1, 6, 6, 9, 9, 9, 9, 9, 9] 149 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 415 number of broken/clashed sets: 148 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220670 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=C(C[NH+](C)C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'S.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 5, 9, 6, 5, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 62, 62, 62, 62, 118, 120, 120, 120, 62, 1, 2, 2, 2, 3, 3, 1, 12, 12, 62, 118, 118, 120, 120, 120, 120, 120, 120] 149 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 379 number of broken/clashed sets: 148 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220670 /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `1' /scratch/stefan/7769890/working/building/REAL300000220670/1 /scratch/stefan/7769890/working/building/REAL300000220670 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/681 `/scratch/stefan/7769890/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=C(CN(C)C)S2)=N1) `REAL300000220670.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220670/1/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: REAL300000220670 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=C(CN(C)C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'S.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 5, 10, 5, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 59, 60, 60, 93, 119, 119, 60, 60, 60, 13, 13, 1, 1, 1, 1, 1, 1, 8, 16, 16, 1, 59, 60, 60, 60, 93, 93, 60, 13, 13, 1, 8, 8, 16, 16, 16, 16, 16, 16] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 437 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220670 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=NC=C(CN(C)C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'S.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 5, 10, 5, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 60, 60, 60, 60, 140, 147, 147, 60, 1, 2, 2, 2, 3, 3, 1, 12, 12, 60, 140, 140, 147, 147, 147, 147, 147, 147] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 476 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220670 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220670 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 1: /scratch/stefan/7769890/working/building/REAL300000220670/1.* 0: /scratch/stefan/7769890/working/building/REAL300000220670/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220670 Building REAL300000220671 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220671' /scratch/stefan/7769890/working/building/REAL300000220671 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220671 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220671/0 /scratch/stefan/7769890/working/building/REAL300000220671 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/682 `/scratch/stefan/7769890/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC=C(Cl)N2C)N1) `REAL300000220671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220671 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC=C(Cl)N2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 16, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [15, 15, 15, 15, 27, 27, 27, 15, 15, 15, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 15, 16, 16, 16, 27, 27, 9, 9, 1, 2, 2, 2, 15] 27 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 111 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: REAL300000220671 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC=C(Cl)N2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 16, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 3, 9, 9, 15, 16, 16, 16, 1] 27 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 20] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220671 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220671 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220671/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220671 Building REAL300000220672 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220672' /scratch/stefan/7769890/working/building/REAL300000220672 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220672 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220672/0 /scratch/stefan/7769890/working/building/REAL300000220672 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/683 `/scratch/stefan/7769890/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC=C2Br)=N1) `REAL300000220672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220672 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 41, 41, 41, 35, 35, 35, 9, 9, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 41, 41, 35, 9, 9, 1, 1] 41 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 89 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220672 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 1, 9, 9, 35, 35] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 76 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220672 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220672 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220672/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220672 Building REAL300000220673 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220673' /scratch/stefan/7769890/working/building/REAL300000220673 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220673 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220673/0 /scratch/stefan/7769890/working/building/REAL300000220673 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/684 `/scratch/stefan/7769890/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(I)=C2)=N1) `REAL300000220673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220673 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(I)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 18, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [18, 18, 18, 18, 33, 33, 33, 18, 18, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 33, 33, 18, 7, 7, 1, 1, 1, 1] 33 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 122 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220673 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(I)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 18, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 7, 7, 1, 1, 1, 1, 1, 7, 7, 18, 18, 13, 18, 18, 18, 1, 2, 2, 2, 3, 3, 1, 7, 7, 18, 18, 18, 18] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 84 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220673 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220673 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220673/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220673 Building REAL300000220674 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220674' /scratch/stefan/7769890/working/building/REAL300000220674 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220674 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220674/0 /scratch/stefan/7769890/working/building/REAL300000220674 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/685 `/scratch/stefan/7769890/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(F)C=CC=C2OC(F)(F)F)=N1) `REAL300000220674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220674 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(F)C=CC=C2OC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 12, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 49, 69, 69, 33, 33, 33, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 33, 33, 33, 33, 49, 49, 33, 7, 7, 1, 1, 1] 71 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 264 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220674 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(F)C=CC=C2OC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 12, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 33, 33, 33, 16, 33, 33, 33, 63, 67, 67, 67, 1, 2, 2, 2, 3, 3, 1, 11, 11, 33, 32, 33] 71 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 228 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220674 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220674 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220674/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220674 Building REAL300000220675 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220675' /scratch/stefan/7769890/working/building/REAL300000220675 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220675 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220675/0 /scratch/stefan/7769890/working/building/REAL300000220675 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/686 `/scratch/stefan/7769890/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)C=C2)=N1) `REAL300000220675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220675 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 12, 12, 12, 17, 22, 22, 12, 12, 12, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 1, 12, 12, 12, 12, 17, 17, 12, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1] 22 rigid atoms, others: [35, 36, 41, 42, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 75 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: REAL300000220675 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 8, 8, 12, 12, 8, 8, 16, 16, 15, 15, 16, 16, 12, 12, 1, 2, 2, 2, 3, 3, 1, 8, 8, 12, 12, 16, 16, 16, 16, 12, 12] 22 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 77 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220675 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(Cl)C=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 22, 22, 22, 16, 16, 16, 5, 5, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 16, 16, 16, 22, 22, 16, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3] 22 rigid atoms, others: [37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 69 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220675 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220675 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220675/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220675 Building REAL300000220676 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220676' /scratch/stefan/7769890/working/building/REAL300000220676 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220676 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220676/0 /scratch/stefan/7769890/working/building/REAL300000220676 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/687 `/scratch/stefan/7769890/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=C(Cl)C=C3)S2)=N1) `REAL300000220676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220676 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=C(Cl)C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 44, 44, 44, 51, 51, 51, 44, 44, 44, 12, 12, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 44, 44, 44, 44, 51, 51, 44, 12, 12, 1, 3, 3, 3, 3] 51 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 115 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: REAL300000220676 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=C(Cl)C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 2, 2, 2, 3, 3, 1, 11, 11, 44, 44, 44, 44, 44] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 87 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220676 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=C(Cl)C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 44, 44, 44, 51, 51, 51, 44, 44, 44, 20, 20, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 44, 44, 44, 44, 51, 51, 44, 20, 20, 3, 1, 1, 1, 1] 51 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 121 number of broken/clashed sets: 50 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220676 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220676 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220676/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220676 Building REAL300000220677 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220677' /scratch/stefan/7769890/working/building/REAL300000220677 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220677 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220677/0 /scratch/stefan/7769890/working/building/REAL300000220677 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/688 `/scratch/stefan/7769890/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)N=C2C=C1) `REAL300000220677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220677 none CC1=CN2C=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [16, 16, 16, 16, 16, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 16, 16, 16, 16, 17, 17, 17, 17, 16, 9, 9, 3, 3, 2, 2, 2, 1, 16, 16] 27 rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220677 none CC1=CN2C=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 16, 16, 16, 16, 16, 27, 27, 27, 16, 16, 16, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 10, 27, 27, 17, 17, 17, 16, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 20, 21, 22, 23, 27, 28, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220677 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220677 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220677/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220677 Building REAL300000220678 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220678' /scratch/stefan/7769890/working/building/REAL300000220678 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220678 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220678/0 /scratch/stefan/7769890/working/building/REAL300000220678 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/689 `/scratch/stefan/7769890/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N(CC3=CC=CC=C3)N=C2)=N1) `REAL300000220678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220678 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N(CC3=CC=CC=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 93, 115, 115, 58, 58, 58, 9, 9, 1, 1, 1, 1, 1, 1, 6, 8, 8, 7, 8, 8, 1, 1, 58, 58, 58, 58, 93, 93, 58, 9, 9, 6, 6, 8, 8, 8, 8, 8, 1] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 402 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220678 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N(CC3=CC=CC=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 58, 58, 58, 58, 137, 158, 158, 147, 158, 158, 58, 58, 1, 2, 2, 2, 3, 3, 1, 11, 11, 137, 137, 158, 158, 158, 158, 158, 58] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 564 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220678 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N(CC3=CC=CC=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 158, 201, 201, 201, 158, 158, 158, 43, 43, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 158, 158, 158, 158, 201, 201, 158, 43, 43, 3, 3, 1, 1, 1, 1, 1, 8] 201 rigid atoms, others: [37, 38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 504 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220678 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220678 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220678/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220678 Building REAL300000220679 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220679' /scratch/stefan/7769890/working/building/REAL300000220679 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220679 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220679/0 /scratch/stefan/7769890/working/building/REAL300000220679 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/690 `/scratch/stefan/7769890/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl) `REAL300000220679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220679 none CC1=CC(Br)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [31, 23, 31, 31, 31, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 11, 11, 2, 2, 2, 3, 3, 1, 31] 37 rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 115 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: REAL300000220679 none CC1=CC(Br)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 37, 37, 37, 31, 31, 31, 1, 1, 1, 2, 2, 2, 1, 7, 7, 31, 31, 31, 37, 37, 31, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220679 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220679 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220679/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220679 Building REAL300000220680 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220680' /scratch/stefan/7769890/working/building/REAL300000220680 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220680 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220680/0 /scratch/stefan/7769890/working/building/REAL300000220680 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/691 `/scratch/stefan/7769890/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=C(F)C=CC=C3F)S2)=N1) `REAL300000220680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220680 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=C(F)C=CC=C3F)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [56, 55, 56, 56, 84, 91, 91, 56, 56, 56, 13, 13, 1, 1, 1, 1, 1, 1, 6, 7, 6, 1, 6, 6, 7, 1, 55, 56, 56, 56, 84, 84, 56, 13, 13, 1, 7, 6, 7] 114 rigid atoms, others: [35, 12, 13, 14, 15, 16, 17, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 305 number of broken/clashed sets: 113 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220680 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=C(F)C=CC=C3F)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 56, 56, 56, 56, 100, 100, 100, 84, 100, 99, 100, 56, 1, 2, 2, 2, 3, 3, 1, 11, 11, 56, 100, 100, 100] 114 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 245 number of broken/clashed sets: 113 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220680 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=C(F)C=CC=C3F)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [100, 100, 100, 100, 114, 114, 114, 100, 100, 100, 39, 39, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 100, 100, 100, 100, 114, 114, 100, 39, 39, 7, 1, 1, 1] 114 rigid atoms, others: [36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 255 number of broken/clashed sets: 113 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220680 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220680 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220680/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220680 Building REAL300000220681 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220681' /scratch/stefan/7769890/working/building/REAL300000220681 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220681 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220681/0 /scratch/stefan/7769890/working/building/REAL300000220681 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/692 `/scratch/stefan/7769890/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Br)=C2F)=N1) `REAL300000220681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220681 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Br)=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [25, 25, 25, 25, 39, 39, 39, 25, 25, 25, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 39, 39, 25, 10, 10, 1, 1, 1] 39 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 127 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220681 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Br)=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 25, 25, 24, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 1, 11, 11, 25, 25, 25] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 73 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220681 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220681 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220681/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220681 Building REAL300000220682 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220682' /scratch/stefan/7769890/working/building/REAL300000220682 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220682 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220682/0 /scratch/stefan/7769890/working/building/REAL300000220682 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/693 `/scratch/stefan/7769890/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3OC=CC3=CC=C2)N1) `REAL300000220682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220682 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3OC=CC3=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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: [39, 39, 39, 39, 48, 48, 48, 39, 39, 39, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 48, 48, 11, 11, 1, 1, 1, 1, 1, 39] 48 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 115 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: REAL300000220682 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3OC=CC3=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 39, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 3, 3, 10, 10, 39, 39, 39, 39, 39, 1] 48 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 78 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220682 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220682 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220682/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220682 Building REAL300000220683 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220683' /scratch/stefan/7769890/working/building/REAL300000220683 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220683 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220683/0 /scratch/stefan/7769890/working/building/REAL300000220683 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/694 `/scratch/stefan/7769890/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=NC(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220683 none CCN1N=NC(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [96, 53, 53, 53, 53, 53, 53, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 96, 96, 96, 96, 96, 53, 53, 53, 11, 11, 3, 3, 2, 2, 2, 1] 109 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 319 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: REAL300000220683 none CCN1N=NC(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 53, 53, 53, 53, 53, 85, 86, 86, 53, 53, 53, 7, 7, 7, 7, 7, 2, 2, 2, 9, 9, 85, 85, 53, 53, 53, 53] 109 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 294 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220683 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220683 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220683/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220683 Building REAL300000220684 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220684' /scratch/stefan/7769890/working/building/REAL300000220684 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220684 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220684/0 /scratch/stefan/7769890/working/building/REAL300000220684 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/695 `/scratch/stefan/7769890/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=CC(Cl)=CN=C3O2)=N1) `REAL300000220684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220684 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=CC(Cl)=CN=C3O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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] 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: [21, 21, 21, 21, 33, 33, 33, 21, 21, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 33, 33, 21, 7, 7, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 106 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: REAL300000220684 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=CC(Cl)=CN=C3O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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] 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 9, 9, 21, 21, 21] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 60 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220684 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220684 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220684/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220684 Building REAL300000220685 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220685' /scratch/stefan/7769890/working/building/REAL300000220685 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220685 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220685/0 /scratch/stefan/7769890/working/building/REAL300000220685 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/696 `/scratch/stefan/7769890/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CC=C3F)S2)=N1) `REAL300000220685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220685 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CC=C3F)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 90, 111, 111, 63, 63, 63, 11, 11, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 12, 1, 63, 63, 63, 63, 90, 90, 63, 11, 11, 1, 12, 12, 12, 12] 201 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 369 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220685 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CC=C3F)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 63, 63, 63, 63, 171, 171, 77, 171, 171, 171, 63, 1, 2, 2, 2, 3, 3, 1, 11, 11, 63, 171, 171, 171, 171] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 558 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220685 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CC=C3F)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 171, 201, 201, 201, 171, 171, 171, 73, 73, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 171, 171, 171, 171, 201, 201, 171, 73, 73, 12, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 477 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220685 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220685 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220685/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220685 Building REAL300000220686 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220686' /scratch/stefan/7769890/working/building/REAL300000220686 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220686 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220686/0 /scratch/stefan/7769890/working/building/REAL300000220686 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/697 `/scratch/stefan/7769890/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(F)=C2Br)=N1) `REAL300000220686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220686 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(F)=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [27, 27, 27, 27, 35, 35, 35, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 35, 35, 27, 7, 7, 1, 1, 1] 35 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 89 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220686 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(F)=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 1, 10, 10, 27, 27, 27] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 70 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220686 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220686 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220686/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220686 Building REAL300000220687 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220687' /scratch/stefan/7769890/working/building/REAL300000220687 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220687 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220687/0 /scratch/stefan/7769890/working/building/REAL300000220687 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/698 `/scratch/stefan/7769890/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=CC=CC=C2C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220687 none COC1=CC2=CC=CC=C2C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [69, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 13, 13, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 69, 69, 69, 57, 57, 57, 57, 57, 57, 13, 13, 3, 3, 2, 2, 2, 1] 89 rigid atoms, others: [42, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 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: REAL300000220687 none COC1=CC2=CC=CC=C2C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 57, 57, 57, 57, 57, 83, 89, 89, 57, 57, 57, 3, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 83, 83, 57, 57, 57, 57] 89 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 33, 29, 30, 31] set([0, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 262 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220687 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220687 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220687/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220687 Building REAL300000220688 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220688' /scratch/stefan/7769890/working/building/REAL300000220688 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220688 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220688/0 /scratch/stefan/7769890/working/building/REAL300000220688 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/699 `/scratch/stefan/7769890/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(N2C=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=N2)C=C1) `REAL300000220688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220688 none COC1=CC=C(N2C=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 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: [6, 6, 2, 6, 6, 1, 1, 1, 1, 1, 7, 7, 38, 38, 38, 38, 38, 57, 78, 78, 38, 38, 38, 1, 1, 6, 6, 7, 7, 7, 6, 6, 1, 7, 7, 38, 38, 38, 57, 57, 38, 1, 6, 6] 78 rigid atoms, others: [32, 5, 6, 7, 8, 9, 41, 23, 24] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 276 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: REAL300000220688 none COC1=CC=C(N2C=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 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, 1, 6, 6, 6, 21, 21, 63, 63, 63, 63, 63, 78, 78, 78, 63, 63, 63, 6, 6, 1, 1, 2, 2, 2, 1, 1, 6, 21, 21, 63, 63, 63, 78, 78, 63, 6, 1, 1] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 43, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220688 none COC1=CC=C(N2C=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 8, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 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: [63, 62, 59, 63, 63, 38, 38, 38, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 38, 38, 63, 63, 63, 63, 63, 63, 63, 38, 11, 11, 2, 2, 2, 3, 3, 1, 38, 63, 63] 78 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 150 number of broken/clashed sets: 77 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220688 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220688 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220688/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220688 Building REAL300000220689 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220689' /scratch/stefan/7769890/working/building/REAL300000220689 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220689 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220689/0 /scratch/stefan/7769890/working/building/REAL300000220689 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/700 `/scratch/stefan/7769890/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220689 none COC1=CC(C)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [61, 49, 49, 49, 40, 49, 49, 49, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 61, 61, 61, 49, 49, 49, 49, 49, 49, 12, 12, 3, 3, 2, 2, 2, 1] 75 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 166 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: REAL300000220689 none COC1=CC(C)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 49, 49, 49, 49, 49, 67, 75, 75, 49, 49, 49, 3, 3, 3, 1, 2, 2, 2, 1, 1, 9, 9, 67, 67, 49, 49, 49, 49] 75 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 30, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 217 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220689 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220689 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220689/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220689 Building REAL300000220690 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220690' /scratch/stefan/7769890/working/building/REAL300000220690 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220690 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220690/0 /scratch/stefan/7769890/working/building/REAL300000220690 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/701 `/scratch/stefan/7769890/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(N(C)C)N=C2)N1) `REAL300000220690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220690 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(N(C)C)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 13, 13, 13, 13, 13, 13, 5, 5, 1, 2, 2, 2, 2, 2, 2, 1, 13] 13 rigid atoms, others: [37, 12, 13, 14, 15, 16, 17, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 27 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: REAL300000220690 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(N(C)C)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 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: [1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 10, 10, 13, 13, 10, 10, 13, 13, 13, 13, 1, 2, 2, 2, 3, 3, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 63 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220690 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220690 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220690/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220690 Building REAL300000220691 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220691' /scratch/stefan/7769890/working/building/REAL300000220691 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220691 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220691/0 /scratch/stefan/7769890/working/building/REAL300000220691 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/702 `/scratch/stefan/7769890/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NC(Cl)=C2F)=N1) `REAL300000220691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220691 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NC(Cl)=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 27, 41, 41, 41, 27, 27, 27, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 41, 41, 27, 10, 10, 1, 1] 41 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 130 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220691 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NC(Cl)=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 1, 11, 11, 27, 27] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 72 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220691 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220691 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220691/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220691 Building REAL300000220692 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220692' /scratch/stefan/7769890/working/building/REAL300000220692 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220692 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220692/0 /scratch/stefan/7769890/working/building/REAL300000220692 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/703 `/scratch/stefan/7769890/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1F) `REAL300000220692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220692 none CC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [28, 28, 13, 28, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 3, 3, 2, 2, 2, 1] 41 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 117 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: REAL300000220692 none CC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 28, 28, 28, 28, 28, 41, 41, 41, 28, 28, 28, 1, 1, 2, 2, 2, 1, 1, 1, 10, 10, 41, 41, 28, 28, 28, 26] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220692 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220692 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220692/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220692 Building REAL300000220693 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220693' /scratch/stefan/7769890/working/building/REAL300000220693 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220693 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220693/0 /scratch/stefan/7769890/working/building/REAL300000220693 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/704 `/scratch/stefan/7769890/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)OCC3=CC=CC=C3)N2)=N1) `REAL300000220693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220693 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)OCC3=CC=CC=C3)N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 59, 97, 97, 30, 30, 30, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 15, 15, 7, 15, 15, 1, 30, 31, 31, 31, 59, 59, 30, 6, 6, 1, 1, 7, 7, 15, 15, 7, 15, 15, 1] 201 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 421 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220693 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)OCC3=CC=CC=C3)N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 30, 30, 30, 30, 52, 52, 52, 92, 157, 157, 92, 157, 157, 30, 1, 2, 2, 2, 3, 3, 1, 9, 9, 30, 30, 92, 92, 157, 157, 92, 157, 157, 28] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 603 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220693 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)OCC3=CC=CC=C3)N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 157, 201, 201, 201, 157, 157, 157, 69, 69, 15, 15, 15, 15, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 15, 157, 157, 157, 157, 201, 201, 157, 69, 69, 15, 15, 4, 4, 1, 1, 1, 1, 1, 15] 201 rigid atoms, others: [41, 42, 43, 44, 45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 568 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220693 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220693 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220693/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220693 Building REAL300000220694 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220694' /scratch/stefan/7769890/working/building/REAL300000220694 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220694 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220694/0 /scratch/stefan/7769890/working/building/REAL300000220694 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/705 `/scratch/stefan/7769890/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CNC(C(=O)OCC3=CC=CC=C3)=C2)=N1) `REAL300000220694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220694 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CNC(C(=O)OCC3=CC=CC=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 78, 117, 117, 46, 46, 46, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 20, 20, 10, 20, 20, 1, 46, 46, 46, 46, 78, 78, 46, 7, 6, 1, 1, 9, 9, 20, 20, 10, 20, 20, 1] 201 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 473 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220694 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CNC(C(=O)OCC3=CC=CC=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 46, 46, 46, 46, 61, 61, 61, 109, 150, 150, 109, 150, 150, 46, 1, 2, 2, 2, 3, 3, 1, 11, 11, 46, 46, 109, 109, 150, 150, 109, 150, 150, 46] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 551 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220694 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CNC(C(=O)OCC3=CC=CC=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 150, 201, 201, 201, 150, 150, 150, 64, 64, 20, 20, 20, 20, 16, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 20, 150, 150, 150, 150, 201, 201, 150, 64, 64, 20, 20, 4, 4, 1, 1, 1, 1, 1, 20] 201 rigid atoms, others: [41, 42, 43, 44, 45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 587 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220694 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220694 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220694/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220694 Building REAL300000220695 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220695' /scratch/stefan/7769890/working/building/REAL300000220695 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220695 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220695/0 /scratch/stefan/7769890/working/building/REAL300000220695 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/706 `/scratch/stefan/7769890/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(I)C=C2)=N1) `REAL300000220695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220695 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(I)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 18, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [8, 8, 8, 8, 14, 14, 14, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 8, 4, 4, 1, 1, 1, 1] 14 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 52 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: REAL300000220695 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(I)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 18, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 3, 3, 1, 8, 8, 8, 8, 8, 8] 14 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 40 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220695 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220695 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220695/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220695 Building REAL300000220696 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220696' /scratch/stefan/7769890/working/building/REAL300000220696 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220696 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220696/0 /scratch/stefan/7769890/working/building/REAL300000220696 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/707 `/scratch/stefan/7769890/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN1C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N=N1) `REAL300000220696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220696 none COC(=O)CN1C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 78, 178, 25, 25, 25, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 24, 25, 178, 178, 178, 78, 78, 25, 12, 12, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 566 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220696 none COC(=O)CN1C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 8, 45, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 24, 24, 38, 57, 57, 25, 25, 25, 1, 1, 45, 45, 45, 8, 8, 1, 6, 6, 25, 25, 25, 38, 38, 25] 201 rigid atoms, others: [4, 5, 6, 7, 8, 22, 23, 29] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 309 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220696 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220696 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220696/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220696 Building REAL300000220697 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220697' /scratch/stefan/7769890/working/building/REAL300000220697 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220697 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220697/0 /scratch/stefan/7769890/working/building/REAL300000220697 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/708 `/scratch/stefan/7769890/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)CC3=CC=CS3)C=C2)=N1) `REAL300000220697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220697 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)CC3=CC=CS3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 14, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 24, 26, 26, 16, 16, 16, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 13, 22, 22, 22, 22, 1, 1, 16, 16, 16, 16, 24, 24, 16, 3, 3, 1, 1, 7, 7, 7, 12, 13, 22, 22, 22, 1, 1] 201 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 46, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 152 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220697 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)CC3=CC=CS3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 14, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 16, 16, 9, 9, 64, 64, 110, 148, 148, 148, 148, 16, 16, 1, 2, 2, 2, 3, 3, 1, 9, 9, 16, 16, 64, 64, 64, 110, 110, 148, 148, 148, 16, 16] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 546 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220697 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(N(C)CC3=CC=CS3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 14, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 201, 201, 201, 148, 148, 148, 38, 38, 17, 9, 22, 22, 9, 5, 9, 1, 1, 1, 1, 1, 1, 22, 22, 148, 148, 148, 148, 201, 201, 148, 38, 38, 22, 22, 9, 9, 9, 5, 5, 1, 1, 1, 22, 22] 201 rigid atoms, others: [43, 44, 45, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 47]) total number of confs: 633 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220697 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220697 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220697/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220697 Building REAL300000220698 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220698' /scratch/stefan/7769890/working/building/REAL300000220698 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220698 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220698/0 /scratch/stefan/7769890/working/building/REAL300000220698 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/709 `/scratch/stefan/7769890/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC2=CC=CC=C21) `REAL300000220698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220698 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 26, 26, 26, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 43, 43, 43, 26, 11, 11, 3, 3, 2, 2, 2, 1, 26, 26, 26, 26, 26] 61 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 100 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: REAL300000220698 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 45, 61, 61, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 7, 7, 45, 45, 26, 26, 26, 26, 1, 1, 1, 1, 1] 61 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 220 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220698 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220698 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220698/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220698 Building REAL300000220699 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220699' /scratch/stefan/7769890/working/building/REAL300000220699 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220699 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220699/0 /scratch/stefan/7769890/working/building/REAL300000220699 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/710 `/scratch/stefan/7769890/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC1=CN=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1) `REAL300000220699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220699 none CSCC1=CN=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 83, 33, 33, 33, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 33, 140, 140, 140, 83, 83, 33, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 388 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220699 none CSCC1=CN=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 1, 1, 1, 1, 1, 1, 8, 8, 33, 33, 33, 33, 33, 56, 79, 79, 34, 34, 34, 1, 21, 21, 21, 7, 7, 1, 8, 8, 34, 34, 34, 56, 56, 34] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 21, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 321 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220699 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220699 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220699/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220699 Building REAL300000220700 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220700' /scratch/stefan/7769890/working/building/REAL300000220700 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220700 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220700/0 /scratch/stefan/7769890/working/building/REAL300000220700 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/711 `/scratch/stefan/7769890/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC(F)F)N=C2)=N1) `REAL300000220700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220700 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC(F)F)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 63, 101, 101, 39, 39, 39, 6, 6, 1, 1, 1, 1, 1, 8, 19, 19, 1, 1, 39, 39, 39, 39, 63, 63, 39, 6, 6, 1, 8, 8, 19, 1] 201 rigid atoms, others: [35, 12, 13, 14, 15, 16, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 420 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220700 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC(F)F)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 15, 15, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 123, 163, 163, 39, 39, 1, 2, 2, 2, 3, 3, 1, 11, 11, 39, 123, 123, 163, 39] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 652 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220700 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220700 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220700/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220700 Building REAL300000220701 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220701' /scratch/stefan/7769890/working/building/REAL300000220701 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220701 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220701/0 /scratch/stefan/7769890/working/building/REAL300000220701 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/712 `/scratch/stefan/7769890/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(F)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220701 none COC1=CC=C(F)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [77, 65, 65, 65, 33, 65, 65, 65, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 77, 77, 77, 65, 35, 65, 11, 11, 3, 3, 2, 2, 2, 1] 98 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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: REAL300000220701 none COC1=CC=C(F)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 65, 65, 65, 65, 65, 92, 98, 98, 65, 65, 65, 4, 4, 4, 1, 1, 1, 11, 11, 92, 92, 65, 65, 65, 65] 98 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 282 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220701 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220701 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220701/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220701 Building REAL300000220702 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220702' /scratch/stefan/7769890/working/building/REAL300000220702 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220702 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220702/0 /scratch/stefan/7769890/working/building/REAL300000220702 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/713 `/scratch/stefan/7769890/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N(C)N=C2)=N1) `REAL300000220702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220702 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N(C)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [32, 32, 32, 32, 39, 39, 39, 32, 32, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 39, 39, 32, 9, 9, 2, 2, 2, 1] 39 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 99 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: REAL300000220702 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)N(C)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 32, 32, 32, 32, 32, 32, 1, 2, 2, 2, 3, 3, 1, 11, 11, 32, 32, 32, 32] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 74 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220702 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220702 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220702/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220702 Building REAL300000220703 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220703' /scratch/stefan/7769890/working/building/REAL300000220703 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220703 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220703/0 /scratch/stefan/7769890/working/building/REAL300000220703 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/714 `/scratch/stefan/7769890/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(F)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220703 none COC1=CC=C(F)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [68, 52, 52, 52, 52, 52, 52, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 52, 68, 68, 68, 52, 52, 12, 12, 3, 3, 2, 2, 2, 1, 52] 92 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 130 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: REAL300000220703 none COC1=CC=C(F)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 52, 52, 52, 52, 52, 72, 84, 84, 52, 52, 52, 1, 3, 3, 3, 1, 1, 11, 11, 72, 72, 52, 52, 52, 46, 1] 92 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 22, 36, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 252 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220703 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220703 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220703/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220703 Building REAL300000220704 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220704' /scratch/stefan/7769890/working/building/REAL300000220704 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220704 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220704/0 /scratch/stefan/7769890/working/building/REAL300000220704 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/715 `/scratch/stefan/7769890/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3CCCC3)C=C2)N1) `REAL300000220704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220704 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3CCCC3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 15, 15, 15, 19, 19, 19, 14, 15, 14, 4, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 15, 15, 15, 15, 19, 19, 4, 4, 1, 1, 6, 6, 6, 6, 6, 6, 7, 6, 6, 1, 1, 15] 56 rigid atoms, others: [32, 33, 44, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 63 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220704 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3CCCC3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 15, 15, 9, 9, 47, 47, 47, 47, 15, 15, 1, 2, 2, 2, 3, 3, 9, 9, 15, 15, 47, 47, 47, 47, 47, 47, 47, 47, 47, 15, 15, 1] 56 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 45, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220704 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3CCCC3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [47, 47, 47, 47, 56, 56, 56, 47, 47, 47, 13, 13, 1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 47, 47, 47, 47, 56, 56, 13, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 47] 56 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 56 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220704 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220704 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220704/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220704 Building REAL300000220705 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220705' /scratch/stefan/7769890/working/building/REAL300000220705 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220705 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220705/0 /scratch/stefan/7769890/working/building/REAL300000220705 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/716 `/scratch/stefan/7769890/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CN=C3O2)N1) `REAL300000220705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220705 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CN=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 4, 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, 29, 29, 29, 37, 37, 37, 29, 29, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 30, 30, 30, 37, 37, 11, 11, 1, 1, 1, 1, 30] 37 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 99 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: REAL300000220705 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=CN=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 1, 2, 2, 2, 3, 3, 11, 11, 29, 29, 29, 29, 1] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 77 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220705 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220705 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220705/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220705 Building REAL300000220706 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220706' /scratch/stefan/7769890/working/building/REAL300000220706 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220706 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220706/0 /scratch/stefan/7769890/working/building/REAL300000220706 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/717 `/scratch/stefan/7769890/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220706 none COC1=CC=CC(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [61, 49, 49, 49, 24, 49, 49, 49, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 61, 61, 61, 49, 48, 49, 49, 49, 49, 11, 11, 3, 3, 2, 2, 2, 1] 80 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300000220706 none COC1=CC=CC(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 49, 49, 49, 49, 49, 76, 80, 80, 49, 49, 49, 3, 3, 3, 1, 1, 1, 2, 2, 2, 9, 9, 76, 76, 49, 49, 49, 49] 80 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220706 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220706 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220706/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220706 Building REAL300000220707 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220707' /scratch/stefan/7769890/working/building/REAL300000220707 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220707 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220707/0 /scratch/stefan/7769890/working/building/REAL300000220707 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/718 `/scratch/stefan/7769890/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=NN(C)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220707 none CCOC(=O)C1=NN(C)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 128, 128, 62, 128, 62, 62, 62, 62, 62, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 154, 154, 154, 154, 154, 62, 62, 62, 62, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 452 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220707 none CCOC(=O)C1=NN(C)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 61, 61, 62, 62, 62, 104, 130, 130, 62, 62, 62, 15, 15, 15, 14, 14, 2, 2, 2, 1, 10, 10, 62, 62, 62, 104, 104, 62] 201 rigid atoms, others: [33, 3, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 504 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220707 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220707 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220707/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220707 Building REAL300000220708 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220708' /scratch/stefan/7769890/working/building/REAL300000220708 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220708 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220708/0 /scratch/stefan/7769890/working/building/REAL300000220708 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/719 `/scratch/stefan/7769890/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)SC2=C(Cl)C=CC=C12) `REAL300000220708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220708 none CC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)SC2=C(Cl)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 1, 1, 16, 1, 1, 1, 1, 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, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 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: [23, 23, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 3, 3, 2, 2, 2, 1, 23, 23, 23] 37 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) 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: REAL300000220708 none CC1=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)SC2=C(Cl)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 1, 1, 16, 1, 1, 1, 1, 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, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 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, 1, 9, 9, 23, 23, 23, 23, 23, 37, 37, 37, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 37, 37, 23, 23, 23, 23, 1, 1, 1] 37 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 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 /scratch/stefan/7769890/working/building/REAL300000220708 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220708 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220708/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220708 Building REAL300000220709 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220709' /scratch/stefan/7769890/working/building/REAL300000220709 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220709 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220709/0 /scratch/stefan/7769890/working/building/REAL300000220709 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/720 `/scratch/stefan/7769890/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2C(F)F)=N1) `REAL300000220709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220709 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2C(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [85, 85, 85, 85, 134, 168, 168, 85, 85, 85, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 85, 85, 85, 85, 134, 134, 85, 11, 11, 1, 2, 2, 2, 12] 179 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 580 number of broken/clashed sets: 178 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220709 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2C(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 85, 85, 85, 85, 85, 85, 156, 156, 1, 2, 2, 2, 3, 3, 1, 12, 12, 85, 85, 85, 85, 156] 179 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 490 number of broken/clashed sets: 178 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220709 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220709 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220709/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220709 Building REAL300000220710 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220710' /scratch/stefan/7769890/working/building/REAL300000220710 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220710 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220710/0 /scratch/stefan/7769890/working/building/REAL300000220710 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/721 `/scratch/stefan/7769890/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3CCC3)C=C2)N1) `REAL300000220710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220710 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3CCC3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 15, 15, 18, 19, 19, 15, 15, 15, 4, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 1, 1, 15, 15, 15, 15, 18, 18, 4, 4, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 15] 51 rigid atoms, others: [32, 40, 41, 12, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 60 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220710 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3CCC3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 15, 15, 10, 10, 46, 46, 46, 15, 15, 1, 2, 2, 2, 3, 3, 10, 10, 15, 15, 46, 46, 46, 46, 46, 46, 46, 15, 15, 1] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 42] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 156 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220710 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3CCC3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [46, 46, 46, 46, 51, 51, 51, 46, 46, 46, 14, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 46, 46, 46, 46, 51, 51, 14, 14, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 46] 51 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42]) total number of confs: 116 number of broken/clashed sets: 51 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220710 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220710 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220710/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220710 Building REAL300000220711 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220711' /scratch/stefan/7769890/working/building/REAL300000220711 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220711 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220711/0 /scratch/stefan/7769890/working/building/REAL300000220711 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/722 `/scratch/stefan/7769890/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC2=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=CC=C12) `REAL300000220711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220711 none COC1=CC=CC2=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [72, 49, 49, 49, 49, 49, 49, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 49, 49, 49, 49, 72, 72, 72, 49, 49, 49, 12, 12, 3, 3, 2, 2, 2, 1, 49, 49, 49] 89 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 142 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: REAL300000220711 none COC1=CC=CC2=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 49, 49, 49, 49, 49, 73, 89, 89, 49, 49, 49, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 73, 73, 49, 49, 49, 49, 1, 1, 1] 89 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 41, 42, 40, 22, 23, 24, 25, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 284 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220711 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220711 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220711/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220711 Building REAL300000220712 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220712' /scratch/stefan/7769890/working/building/REAL300000220712 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220712 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220712/0 /scratch/stefan/7769890/working/building/REAL300000220712 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/723 `/scratch/stefan/7769890/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=N1) `REAL300000220712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220712 none COC1=NC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [68, 47, 47, 47, 47, 47, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 47, 68, 68, 68, 48, 48, 12, 12, 3, 3, 2, 2, 2, 1] 89 rigid atoms, others: [34, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 140 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: REAL300000220712 none COC1=NC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 47, 47, 47, 47, 47, 70, 74, 74, 47, 47, 47, 1, 3, 3, 3, 1, 1, 11, 11, 70, 70, 48, 48, 48, 47] 89 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 228 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220712 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220712 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220712/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220712 Building REAL300000220713 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220713' /scratch/stefan/7769890/working/building/REAL300000220713 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220713 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220713/0 /scratch/stefan/7769890/working/building/REAL300000220713 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/724 `/scratch/stefan/7769890/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2=CC=NN2C)N1) `REAL300000220713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220713 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2=CC=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 114, 125, 125, 72, 72, 72, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 72, 72, 72, 72, 114, 114, 10, 10, 1, 1, 1, 1, 7, 7, 7, 7, 7, 72] 150 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 395 number of broken/clashed sets: 149 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220713 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2=CC=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 72, 72, 71, 72, 72, 72, 108, 108, 108, 108, 108, 1, 2, 2, 2, 3, 3, 12, 12, 72, 72, 72, 72, 108, 108, 108, 108, 108, 1] 150 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 42] set([4, 5, 6, 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, 39, 40, 41]) total number of confs: 196 number of broken/clashed sets: 149 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220713 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C2=CC=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 150, 150, 150, 108, 108, 108, 29, 29, 7, 7, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 150, 150, 29, 29, 7, 7, 7, 7, 1, 1, 2, 2, 2, 108] 150 rigid atoms, others: [37, 38, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 427 number of broken/clashed sets: 149 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220713 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220713 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220713/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220713 Building REAL300000220714 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220714' /scratch/stefan/7769890/working/building/REAL300000220714 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220714 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220714/0 /scratch/stefan/7769890/working/building/REAL300000220714 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/725 `/scratch/stefan/7769890/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3ON=CC3=C2)N1) `REAL300000220714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220714 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3ON=CC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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, 16, 27, 27, 27, 16, 16, 16, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 27, 27, 7, 7, 1, 1, 1, 1, 16] 27 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 94 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: REAL300000220714 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3ON=CC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 3, 3, 9, 9, 16, 16, 16, 16, 1] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 52 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220714 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220714 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220714/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220714 Building REAL300000220715 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220715' /scratch/stefan/7769890/working/building/REAL300000220715 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220715 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220715/0 /scratch/stefan/7769890/working/building/REAL300000220715 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/726 `/scratch/stefan/7769890/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N1C) `REAL300000220715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220715 none COC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [113, 113, 61, 113, 61, 61, 61, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 61, 61, 113, 113, 113, 61, 61, 12, 12, 3, 3, 2, 2, 2, 1, 61, 61, 61] 158 rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 286 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: REAL300000220715 none COC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [13, 13, 1, 13, 1, 1, 1, 1, 1, 10, 10, 61, 61, 61, 61, 61, 103, 112, 112, 61, 61, 61, 1, 1, 13, 13, 13, 1, 1, 10, 10, 103, 103, 61, 61, 61, 61, 2, 2, 2] 158 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 401 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220715 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220715 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220715/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220715 Building REAL300000220716 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220716' /scratch/stefan/7769890/working/building/REAL300000220716 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220716 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220716/0 /scratch/stefan/7769890/working/building/REAL300000220716 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/727 `/scratch/stefan/7769890/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC3=C(F)C(F)=CC=C3C=C2)N1) `REAL300000220716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220716 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC3=C(F)C(F)=CC=C3C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 15, 1, 15, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [31, 31, 31, 31, 39, 39, 39, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 32, 32, 32, 39, 39, 9, 9, 1, 1, 1, 1, 31] 39 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 37, 32, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 101 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: REAL300000220716 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NC3=C(F)C(F)=CC=C3C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 15, 1, 15, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 9, 9, 31, 31, 31, 31, 1] 39 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 25] set([4, 5, 6, 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: 75 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220716 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220716 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220716/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220716 Building REAL300000220717 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220717' /scratch/stefan/7769890/working/building/REAL300000220717 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220717 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220717/0 /scratch/stefan/7769890/working/building/REAL300000220717 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/728 `/scratch/stefan/7769890/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC=C1C=C(C)C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220717 none COCC1=CC=CC=C1C=C(C)C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 140, 57, 57, 57, 25, 57, 57, 25, 25, 12, 25, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 163, 163, 163, 140, 140, 57, 41, 57, 57, 25, 25, 25, 25, 12, 12, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 46, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 681 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220717 none COCC1=CC=CC=C1C=C(C)C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 57, 57, 57, 57, 57, 102, 147, 147, 57, 57, 57, 22, 22, 22, 7, 7, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 57, 57, 57, 102, 102, 57] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 574 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220717 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220717 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220717/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220717 Building REAL300000220718 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220718' /scratch/stefan/7769890/working/building/REAL300000220718 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220718 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220718/0 /scratch/stefan/7769890/working/building/REAL300000220718 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/729 `/scratch/stefan/7769890/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=NN(C)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220718 none COC(=O)C1=NN(C)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 66, 148, 66, 66, 66, 66, 66, 66, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 148, 148, 148, 66, 66, 66, 66, 66, 66, 12, 12, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [41, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 372 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220718 none COC(=O)C1=NN(C)C(C)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 66, 66, 66, 66, 66, 117, 134, 134, 66, 66, 66, 11, 11, 11, 2, 2, 2, 2, 2, 2, 9, 9, 66, 66, 66, 117, 117, 66] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 492 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220718 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220718 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220718/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220718 Building REAL300000220719 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220719' /scratch/stefan/7769890/working/building/REAL300000220719 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220719 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220719/0 /scratch/stefan/7769890/working/building/REAL300000220719 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/730 `/scratch/stefan/7769890/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220719 none CC1=CC(Cl)=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [20, 20, 18, 20, 20, 20, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 20, 20, 20, 20, 19, 20, 11, 11, 3, 3, 1, 1, 1, 1, 20] 33 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 58 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: REAL300000220719 none CC1=CC(Cl)=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 33, 33, 33, 20, 20, 20, 1, 2, 2, 2, 1, 1, 6, 6, 33, 33, 20, 20, 20, 20, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220719 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220719 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220719/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220719 Building REAL300000220720 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220720' /scratch/stefan/7769890/working/building/REAL300000220720 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220720 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220720/0 /scratch/stefan/7769890/working/building/REAL300000220720 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/731 `/scratch/stefan/7769890/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CON=C2CC2=CC=CC=C2)=N1) `REAL300000220720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220720 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CON=C2CC2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 12, 8, 1, 5, 1, 1, 1, 1, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 100, 133, 133, 55, 55, 55, 9, 9, 1, 1, 1, 1, 1, 1, 1, 8, 10, 10, 9, 10, 10, 55, 55, 55, 55, 100, 100, 55, 9, 9, 1, 8, 8, 10, 10, 10, 10, 10] 201 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 507 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220720 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CON=C2CC2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 12, 8, 1, 5, 1, 1, 1, 1, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 55, 55, 55, 55, 55, 123, 128, 128, 126, 128, 128, 1, 2, 2, 2, 3, 3, 1, 11, 11, 55, 123, 123, 128, 128, 128, 128, 128] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 437 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220720 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CON=C2CC2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 12, 8, 1, 5, 1, 1, 1, 1, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 128, 201, 201, 201, 128, 128, 128, 39, 39, 10, 10, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 201, 201, 128, 39, 39, 10, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 650 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220720 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220720 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220720/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220720 Building REAL300000220721 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220721' /scratch/stefan/7769890/working/building/REAL300000220721 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220721 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220721/0 /scratch/stefan/7769890/working/building/REAL300000220721 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/732 `/scratch/stefan/7769890/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(O)=C2Cl)N1) `REAL300000220721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220721 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(O)=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [32, 32, 32, 32, 35, 35, 35, 32, 32, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 35, 35, 9, 9, 1, 1, 1, 2, 31] 70 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 70 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220721 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(O)=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 32, 32, 32, 32, 32, 32, 32, 1, 2, 2, 2, 3, 3, 11, 11, 32, 32, 32, 64, 1] 70 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 140 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220721 /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `1' /scratch/stefan/7769890/working/building/REAL300000220721/1 /scratch/stefan/7769890/working/building/REAL300000220721 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/733 `/scratch/stefan/7769890/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC([O-])=C2Cl)N1) `REAL300000220721.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220721/1/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: REAL300000220721 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC([O-])=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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: [31, 31, 31, 31, 39, 39, 39, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 39, 39, 9, 9, 1, 1, 1, 30] 39 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 98 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220721 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC([O-])=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 31, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 12, 12, 31, 31, 31, 1] 39 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 79 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220721 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220721 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 1: /scratch/stefan/7769890/working/building/REAL300000220721/1.* 0: /scratch/stefan/7769890/working/building/REAL300000220721/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220721 Building REAL300000220722 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220722' /scratch/stefan/7769890/working/building/REAL300000220722 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220722 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220722/0 /scratch/stefan/7769890/working/building/REAL300000220722 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/734 `/scratch/stefan/7769890/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220722 none COCCOCC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 136, 98, 41, 41, 11, 11, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 21, 21, 145, 145, 145, 136, 136, 98, 98, 41, 41, 21, 21, 6, 6, 2, 2, 2, 3, 3, 1, 21, 21] 201 rigid atoms, others: [44, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 726 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220722 none COCCOCC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 40, 67, 67, 21, 21, 21, 1, 1, 31, 31, 31, 17, 17, 9, 9, 3, 3, 1, 1, 5, 5, 21, 21, 21, 40, 40, 21, 1, 1] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 346 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220722 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220722 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220722/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220722 Building REAL300000220723 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220723' /scratch/stefan/7769890/working/building/REAL300000220723 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220723 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220723/0 /scratch/stefan/7769890/working/building/REAL300000220723 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/735 `/scratch/stefan/7769890/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(O)=CC(C(F)(F)F)=C2)=N1) `REAL300000220723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220723 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(O)=CC(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [23, 23, 23, 23, 34, 34, 34, 23, 23, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 23, 23, 23, 23, 34, 34, 23, 6, 6, 1, 2, 1, 1] 68 rigid atoms, others: [33, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34]) total number of confs: 108 number of broken/clashed sets: 68 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220723 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(O)=CC(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 3, 1, 10, 10, 23, 46, 23, 23] 68 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 110 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220723 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220723 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220723/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220723 Building REAL300000220724 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220724' /scratch/stefan/7769890/working/building/REAL300000220724 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220724 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220724/0 /scratch/stefan/7769890/working/building/REAL300000220724 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/736 `/scratch/stefan/7769890/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(N(C)C)N2C)N1) `REAL300000220724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220724 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(N(C)C)N2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 48, 48, 48, 71, 71, 71, 48, 48, 48, 10, 10, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 48, 48, 48, 48, 71, 71, 10, 10, 1, 4, 4, 4, 4, 4, 4, 2, 2, 2, 48] 71 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 218 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220724 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(N(C)C)N2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 48, 48, 48, 48, 63, 63, 48, 48, 1, 2, 2, 2, 3, 3, 11, 11, 48, 63, 63, 63, 63, 63, 63, 48, 48, 48, 1] 71 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 40, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 158 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220724 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220724 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220724/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220724 Building REAL300000220725 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220725' /scratch/stefan/7769890/working/building/REAL300000220725 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220725 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220725/0 /scratch/stefan/7769890/working/building/REAL300000220725 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/737 `/scratch/stefan/7769890/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3CCCCC3=C2)N1) `REAL300000220725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220725 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3CCCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 18, 27, 27, 27, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 27, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18] 27 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 42, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 83 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: REAL300000220725 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3CCCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 3, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 42] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 57 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220725 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220725 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220725/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220725 Building REAL300000220726 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220726' /scratch/stefan/7769890/working/building/REAL300000220726 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220726 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220726/0 /scratch/stefan/7769890/working/building/REAL300000220726 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/738 `/scratch/stefan/7769890/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C)=C1OC) `REAL300000220726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220726 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [91, 53, 53, 53, 53, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 53, 53, 53, 53, 87, 91, 91, 91, 53, 53, 12, 12, 3, 3, 2, 2, 2, 1, 53, 53, 53, 87, 87, 87] 119 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 223 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: REAL300000220726 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.3', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 53, 53, 53, 53, 53, 83, 91, 91, 53, 53, 53, 1, 1, 1, 1, 4, 3, 3, 3, 1, 1, 9, 9, 83, 83, 53, 53, 53, 49, 2, 2, 2, 5, 5, 5] 119 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 307 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220726 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220726 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220726/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220726 Building REAL300000220727 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220727' /scratch/stefan/7769890/working/building/REAL300000220727 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220727 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220727/0 /scratch/stefan/7769890/working/building/REAL300000220727 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/739 `/scratch/stefan/7769890/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC=C2C(F)(F)F)=N1) `REAL300000220727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220727 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC=C2C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [35, 35, 35, 35, 49, 49, 49, 35, 35, 35, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 35, 35, 35, 35, 49, 49, 32, 7, 7, 1, 1] 49 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 142 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: REAL300000220727 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC=C2C(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 1, 11, 11, 35, 35] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 81 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220727 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220727 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220727/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220727 Building REAL300000220728 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220728' /scratch/stefan/7769890/working/building/REAL300000220728 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220728 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220728/0 /scratch/stefan/7769890/working/building/REAL300000220728 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/740 `/scratch/stefan/7769890/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1)=CC1=CC=CC=C1OC(F)F) `REAL300000220728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220728 none CC(C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1)=CC1=CC=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 8, 8, 49, 49, 49, 49, 49, 84, 129, 129, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 4, 4, 4, 8, 8, 49, 49, 49, 84, 84, 49, 4, 1, 1, 1, 1, 21] 201 rigid atoms, others: [39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43]) total number of confs: 523 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220728 none CC(C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1)=CC1=CC=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 23, 23, 49, 49, 42, 49, 49, 49, 101, 142, 142, 24, 24, 24, 11, 11, 2, 2, 2, 3, 3, 1, 23, 49, 49, 49, 49, 142] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 37] set([0, 1, 2, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 478 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220728 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220728 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220728/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220728 Building REAL300000220729 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220729' /scratch/stefan/7769890/working/building/REAL300000220729 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220729 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220729/0 /scratch/stefan/7769890/working/building/REAL300000220729 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/741 `/scratch/stefan/7769890/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC(Cl)=C2[N+](=O)[O-])=N1) `REAL300000220729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220729 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC(Cl)=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 39, 39, 39, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 29, 29, 29, 29, 39, 39, 29, 5, 5, 1, 1] 39 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 103 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220729 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=CC(Cl)=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 2, 2, 2, 3, 3, 1, 11, 11, 29, 29] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220729 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220729 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220729/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220729 Building REAL300000220730 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220730' /scratch/stefan/7769890/working/building/REAL300000220730 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220730 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220730/0 /scratch/stefan/7769890/working/building/REAL300000220730 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/742 `/scratch/stefan/7769890/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN3C=CC(Br)=CC3=N2)=N1) `REAL300000220730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220730 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN3C=CC(Br)=CC3=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 17, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 20, 36, 36, 36, 20, 20, 20, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 36, 36, 20, 9, 9, 1, 1, 1, 1] 36 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 132 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220730 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN3C=CC(Br)=CC3=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 17, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 1, 9, 9, 20, 20, 20, 20] 36 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 60 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220730 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220730 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220730/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220730 Building REAL300000220731 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220731' /scratch/stefan/7769890/working/building/REAL300000220731 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220731 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220731/0 /scratch/stefan/7769890/working/building/REAL300000220731 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/743 `/scratch/stefan/7769890/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CN=C2N(C)C)N1) `REAL300000220731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220731 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CN=C2N(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 71, 71, 71, 45, 45, 45, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 45, 45, 45, 45, 71, 71, 10, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 45] 71 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 230 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220731 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CN=C2N(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 45, 45, 45, 45, 45, 45, 50, 50, 1, 2, 2, 2, 3, 3, 10, 10, 45, 45, 45, 50, 50, 50, 50, 50, 50, 1] 71 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 112 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220731 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220731 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220731/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220731 Building REAL300000220732 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220732' /scratch/stefan/7769890/working/building/REAL300000220732 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220732 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220732/0 /scratch/stefan/7769890/working/building/REAL300000220732 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/744 `/scratch/stefan/7769890/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1N1C=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N=N1) `REAL300000220732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220732 none CC1=CC=CC=C1N1C=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [8, 8, 8, 1, 8, 8, 1, 1, 1, 1, 1, 13, 13, 52, 52, 53, 53, 53, 80, 83, 83, 53, 53, 53, 1, 1, 8, 8, 8, 8, 1, 8, 8, 1, 13, 13, 80, 80, 53, 53, 53, 53] 113 rigid atoms, others: [33, 6, 7, 8, 9, 10, 24, 25] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) 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: REAL300000220732 none CC1=CC=CC=C1N1C=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 1, 1, 1, 8, 8, 8, 46, 46, 84, 84, 84, 84, 84, 113, 113, 113, 84, 84, 84, 8, 8, 2, 2, 2, 1, 1, 1, 1, 8, 46, 46, 113, 113, 84, 84, 84, 84] 113 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 29, 30, 31] set([8, 9, 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, 39, 40, 41]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220732 none CC1=CC=CC=C1N1C=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [84, 84, 84, 53, 84, 84, 53, 53, 53, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 53, 53, 84, 84, 84, 84, 59, 84, 84, 53, 10, 10, 3, 3, 2, 2, 2, 1] 113 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 223 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220732 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220732 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220732/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220732 Building REAL300000220733 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220733' /scratch/stefan/7769890/working/building/REAL300000220733 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220733 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220733/0 /scratch/stefan/7769890/working/building/REAL300000220733 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/745 `/scratch/stefan/7769890/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C([N+](=O)[O-])C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220733 none COC(=O)C1=CC=C([N+](=O)[O-])C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 40, 137, 40, 40, 40, 40, 40, 40, 40, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 40, 137, 137, 137, 40, 40, 12, 12, 2, 2, 2, 3, 3, 1, 40] 166 rigid atoms, others: [39, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 348 number of broken/clashed sets: 165 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220733 none COC(=O)C1=CC=C([N+](=O)[O-])C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 5, 40, 40, 40, 40, 40, 66, 114, 114, 40, 40, 40, 1, 13, 13, 13, 1, 1, 5, 5, 40, 40, 40, 66, 66, 40, 1] 166 rigid atoms, others: [2, 4, 5, 6, 7, 8, 11, 12, 40, 26, 30, 31] set([0, 1, 3, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 424 number of broken/clashed sets: 165 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220733 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220733 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220733/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220733 Building REAL300000220734 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220734' /scratch/stefan/7769890/working/building/REAL300000220734 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220734 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220734/0 /scratch/stefan/7769890/working/building/REAL300000220734 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/746 `/scratch/stefan/7769890/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCCCCl)C=C2)=N1) `REAL300000220734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220734 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCCCCl)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 16, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 27, 47, 47, 15, 15, 15, 3, 3, 1, 1, 1, 1, 1, 1, 7, 11, 26, 35, 1, 1, 15, 15, 15, 15, 27, 27, 15, 3, 3, 1, 1, 11, 11, 26, 26, 35, 35, 1, 1] 201 rigid atoms, others: [33, 34, 41, 42, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 328 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220734 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OCCCCl)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 16, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 10, 10, 15, 15, 10, 10, 59, 73, 133, 159, 15, 15, 1, 2, 2, 2, 3, 3, 1, 10, 10, 15, 15, 73, 73, 133, 133, 159, 159, 15, 15] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 666 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220734 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220734 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220734/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220734 Building REAL300000220735 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220735' /scratch/stefan/7769890/working/building/REAL300000220735 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220735 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220735/0 /scratch/stefan/7769890/working/building/REAL300000220735 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/747 `/scratch/stefan/7769890/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=N1) `REAL300000220735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220735 none COC(=O)C1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 62, 133, 62, 61, 62, 62, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 62, 133, 133, 133, 61, 62, 62, 11, 11, 2, 2, 2, 3, 3, 1] 164 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 331 number of broken/clashed sets: 163 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220735 none COC(=O)C1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 61, 61, 62, 62, 62, 98, 114, 114, 62, 62, 62, 1, 13, 13, 13, 1, 1, 1, 11, 11, 62, 62, 62, 98, 98, 62] 164 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23, 27, 28, 29] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 397 number of broken/clashed sets: 163 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220735 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220735 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220735/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220735 Building REAL300000220736 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220736' /scratch/stefan/7769890/working/building/REAL300000220736 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220736 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220736/0 /scratch/stefan/7769890/working/building/REAL300000220736 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/748 `/scratch/stefan/7769890/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(F)=C2C#N)N1) `REAL300000220736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220736 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(F)=C2C#N)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.1', 'N.1', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [32, 32, 32, 32, 43, 43, 43, 32, 32, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 43, 43, 9, 9, 1, 1, 1, 32] 43 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 116 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: REAL300000220736 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(F)=C2C#N)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.1', 'N.1', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 1, 2, 2, 2, 3, 3, 10, 10, 32, 32, 32, 1] 43 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 75 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220736 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220736 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220736/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220736 Building REAL300000220737 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220737' /scratch/stefan/7769890/working/building/REAL300000220737 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220737 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220737/0 /scratch/stefan/7769890/working/building/REAL300000220737 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/749 `/scratch/stefan/7769890/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=NC=C2F)=N1) `REAL300000220737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220737 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=NC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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: [30, 30, 30, 30, 45, 45, 45, 30, 30, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 45, 45, 30, 10, 10, 1, 1] 45 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 138 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: REAL300000220737 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=NC=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 30, 30, 30, 30, 30, 30, 30, 1, 2, 2, 2, 3, 3, 1, 11, 11, 30, 30] 45 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220737 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220737 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220737/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220737 Building REAL300000220738 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220738' /scratch/stefan/7769890/working/building/REAL300000220738 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220738 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220738/0 /scratch/stefan/7769890/working/building/REAL300000220738 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/750 `/scratch/stefan/7769890/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)N2)=N1) `REAL300000220738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220738 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [32, 32, 32, 32, 41, 41, 41, 32, 32, 32, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 32, 32, 32, 32, 41, 41, 32, 11, 11, 1, 1, 1] 41 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 113 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220738 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 1, 2, 2, 2, 3, 3, 1, 10, 10, 32, 32, 32] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 75 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220738 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220738 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220738/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220738 Building REAL300000220739 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220739' /scratch/stefan/7769890/working/building/REAL300000220739 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220739 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220739/0 /scratch/stefan/7769890/working/building/REAL300000220739 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/751 `/scratch/stefan/7769890/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CNC(C(F)(F)F)=C2)=N1) `REAL300000220739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220739 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CNC(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 4, 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, 22, 22, 22, 30, 30, 30, 22, 22, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 30, 30, 22, 7, 7, 1, 1, 1] 30 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 84 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220739 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CNC(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 1, 11, 11, 22, 22, 22] 30 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 61 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220739 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220739 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220739/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220739 Building REAL300000220740 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220740' /scratch/stefan/7769890/working/building/REAL300000220740 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220740 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220740/0 /scratch/stefan/7769890/working/building/REAL300000220740 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/752 `/scratch/stefan/7769890/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1) `REAL300000220740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220740 none CC1=CC(Br)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [33, 33, 33, 33, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 33, 33, 33, 33, 33, 9, 9, 2, 2, 2, 3, 3, 1] 39 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 74 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: REAL300000220740 none CC1=CC(Br)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 33, 33, 33, 33, 33, 39, 39, 39, 33, 33, 33, 1, 2, 2, 2, 1, 9, 9, 33, 33, 33, 39, 39, 33] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 93 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220740 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220740 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220740/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220740 Building REAL300000220741 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220741' /scratch/stefan/7769890/working/building/REAL300000220741 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220741 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220741/0 /scratch/stefan/7769890/working/building/REAL300000220741 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/753 `/scratch/stefan/7769890/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCCC(=O)[O-])=N1) `REAL300000220741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220741 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCCC(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 49, 89, 89, 36, 36, 36, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 30, 50, 40, 36, 36, 36, 36, 49, 49, 36, 9, 9, 1, 1, 1, 1, 27, 27, 29, 29] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 433 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220741 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCCC(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 36, 36, 20, 36, 36, 36, 81, 174, 176, 187, 180, 1, 2, 2, 2, 3, 3, 1, 9, 9, 36, 36, 36, 36, 174, 174, 176, 176] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 691 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220741 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220741 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220741/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220741 Building REAL300000220742 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220742' /scratch/stefan/7769890/working/building/REAL300000220742 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220742 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220742/0 /scratch/stefan/7769890/working/building/REAL300000220742 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/754 `/scratch/stefan/7769890/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC(N)=O)N=N2)=N1) `REAL300000220742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220742 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC(N)=O)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 8, 11, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 40, 40, 61, 97, 97, 41, 41, 41, 6, 6, 1, 1, 1, 1, 1, 9, 44, 44, 1, 1, 41, 41, 41, 41, 61, 61, 41, 6, 6, 1, 9, 9, 44, 44] 201 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 429 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220742 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC(N)=O)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 8, 11, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 41, 41, 41, 117, 163, 163, 41, 40, 1, 2, 2, 2, 3, 3, 1, 12, 12, 41, 117, 117, 163, 163] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 570 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220742 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220742 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220742/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220742 Building REAL300000220743 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220743' /scratch/stefan/7769890/working/building/REAL300000220743 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220743 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220743/0 /scratch/stefan/7769890/working/building/REAL300000220743 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/755 `/scratch/stefan/7769890/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Cl)=C1) `REAL300000220743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220743 none CC1=CC(F)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [17, 17, 17, 17, 17, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 9, 9, 2, 2, 2, 3, 3, 1, 17] 31 rigid atoms, others: [34, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 58 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: REAL300000220743 none CC1=CC(F)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 1, 7, 7, 17, 17, 17, 17, 17, 31, 31, 31, 17, 17, 17, 1, 1, 1, 2, 2, 2, 1, 7, 7, 17, 17, 17, 31, 31, 17, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 121 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220743 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220743 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220743/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220743 Building REAL300000220744 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220744' /scratch/stefan/7769890/working/building/REAL300000220744 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220744 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220744/0 /scratch/stefan/7769890/working/building/REAL300000220744 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/756 `/scratch/stefan/7769890/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(O)=C2Br)=N1) `REAL300000220744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220744 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(O)=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 35, 35, 35, 26, 26, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 35, 35, 26, 7, 7, 1, 1, 1, 2] 70 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 96 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220744 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(O)=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 26, 26, 26, 26, 26, 26, 26, 1, 2, 2, 2, 3, 3, 1, 10, 10, 26, 26, 26, 52] 70 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 121 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220744 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220744 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220744/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220744 Building REAL300000220745 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220745' /scratch/stefan/7769890/working/building/REAL300000220745 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220745 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220745/0 /scratch/stefan/7769890/working/building/REAL300000220745 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/757 `/scratch/stefan/7769890/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3CC3)C=C2)N1) `REAL300000220745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220745 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3CC3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 25, 25, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 5, 5, 5, 5, 5, 1, 1, 13] 49 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 39]) total number of confs: 77 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: REAL300000220745 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3CC3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 13, 13, 9, 9, 49, 49, 13, 13, 1, 2, 2, 2, 3, 3, 9, 9, 13, 13, 49, 49, 49, 49, 49, 13, 13, 1] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220745 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3CC3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 49, 49, 49, 49, 49, 49, 49, 9, 9, 1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 49, 49, 49, 49, 49, 49, 9, 9, 5, 5, 1, 1, 1, 1, 1, 5, 5, 49] 49 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, 39]) total number of confs: 78 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220745 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220745 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220745/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220745 Building REAL300000220746 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220746' /scratch/stefan/7769890/working/building/REAL300000220746 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220746 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220746/0 /scratch/stefan/7769890/working/building/REAL300000220746 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/758 `/scratch/stefan/7769890/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(S(N)(=O)=O)=C2)=N1) `REAL300000220746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220746 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(S(N)(=O)=O)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 43, 51, 51, 28, 28, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 28, 28, 28, 28, 43, 43, 28, 5, 5, 1, 1, 4, 4, 1] 97 rigid atoms, others: [33, 34, 37, 12, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 172 number of broken/clashed sets: 97 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220746 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(S(N)(=O)=O)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 28, 28, 18, 27, 28, 28, 68, 68, 68, 28, 1, 2, 2, 2, 3, 3, 1, 9, 9, 28, 28, 68, 68, 28] 97 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 313 number of broken/clashed sets: 97 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220746 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220746 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220746/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220746 Building REAL300000220747 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220747' /scratch/stefan/7769890/working/building/REAL300000220747 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220747 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220747/0 /scratch/stefan/7769890/working/building/REAL300000220747 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/759 `/scratch/stefan/7769890/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(N)(=O)=O)C(Cl)=C2)=N1) `REAL300000220747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220747 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(N)(=O)=O)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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, 25, 25, 37, 49, 49, 25, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 25, 25, 25, 25, 37, 37, 25, 6, 6, 1, 1, 4, 4, 1] 81 rigid atoms, others: [33, 34, 37, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 170 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220747 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(N)(=O)=O)C(Cl)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 25, 55, 55, 55, 25, 25, 25, 1, 2, 2, 2, 3, 3, 1, 9, 9, 25, 25, 55, 55, 25] 81 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 203 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220747 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220747 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220747/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220747 Building REAL300000220748 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220748' /scratch/stefan/7769890/working/building/REAL300000220748 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220748 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220748/0 /scratch/stefan/7769890/working/building/REAL300000220748 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/760 `/scratch/stefan/7769890/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C=C2C(=C1)N=CN2C(C#N)=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220748 none CC1=C(C)C=C2C(=C1)N=CN2C(C#N)=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.1', 'N.1', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 1, 1, 1, 8, 1, 8, 1, 1, 8, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 9, 9, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 9, 3, 3, 2, 2, 2, 1] 82 rigid atoms, others: [42, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) 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: REAL300000220748 none CC1=C(C)C=C2C(=C1)N=CN2C(C#N)=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.1', 'N.1', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 1, 1, 1, 8, 1, 8, 1, 1, 8, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 53, 53, 53, 53, 53, 82, 82, 82, 53, 53, 53, 2, 2, 2, 2, 2, 2, 1, 1, 1, 12, 82, 82, 53, 53, 53, 53] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 33] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 263 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220748 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220748 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220748/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220748 Building REAL300000220749 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220749' /scratch/stefan/7769890/working/building/REAL300000220749 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220749 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220749/0 /scratch/stefan/7769890/working/building/REAL300000220749 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/761 `/scratch/stefan/7769890/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=CC=CC=C2C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220749 none COC1=CC=C(C2=CC=CC=C2C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 38, 38, 132, 132, 132, 132, 132, 179, 201, 201, 132, 132, 132, 15, 15, 15, 7, 7, 1, 1, 1, 1, 2, 2, 2, 7, 38, 38, 179, 179, 132, 132, 132, 132] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 595 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220749 none COC1=CC=C(C2=CC=CC=C2C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 1, 1, 1, 9, 9, 54, 54, 54, 54, 54, 81, 101, 101, 54, 54, 54, 4, 4, 4, 1, 1, 7, 7, 2, 7, 7, 7, 7, 1, 9, 9, 81, 81, 54, 54, 54, 54] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 41, 13, 14, 15] set([0, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 340 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: REAL300000220749 none COC1=CC=C(C2=CC=CC=C2C)C=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 54, 54, 54, 54, 54, 54, 132, 132, 89, 132, 132, 132, 54, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 75, 75, 75, 54, 54, 132, 132, 103, 132, 132, 132, 132, 54, 11, 11, 3, 3, 2, 2, 2, 1] 201 rigid atoms, others: [49, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 382 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220749 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220749 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220749/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220749 Building REAL300000220750 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220750' /scratch/stefan/7769890/working/building/REAL300000220750 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220750 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220750/0 /scratch/stefan/7769890/working/building/REAL300000220750 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/762 `/scratch/stefan/7769890/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C(F)C=C2)N1) `REAL300000220750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220750 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C(F)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 132, 153, 153, 86, 87, 86, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 2, 7, 7, 87, 87, 87, 87, 132, 132, 12, 12, 1, 2, 2, 2, 7, 7, 7, 7, 87] 159 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 491 number of broken/clashed sets: 158 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220750 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C(F)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 87, 87, 87, 87, 87, 87, 135, 135, 109, 113, 135, 135, 1, 2, 2, 2, 3, 3, 12, 12, 87, 87, 87, 87, 135, 135, 135, 135, 1] 159 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 26, 42] set([4, 5, 6, 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, 41]) total number of confs: 304 number of broken/clashed sets: 158 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220750 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC=C(F)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 135, 159, 159, 159, 135, 135, 135, 40, 40, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 159, 159, 40, 40, 7, 7, 7, 7, 1, 1, 1, 1, 135] 159 rigid atoms, others: [38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 356 number of broken/clashed sets: 158 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220750 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220750 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220750/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220750 Building REAL300000220751 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220751' /scratch/stefan/7769890/working/building/REAL300000220751 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220751 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220751/0 /scratch/stefan/7769890/working/building/REAL300000220751 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/763 `/scratch/stefan/7769890/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC3=C2OC(F)(F)O3)=N1) `REAL300000220751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220751 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC3=C2OC(F)(F)O3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [38, 38, 38, 38, 53, 53, 53, 38, 38, 38, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 53, 53, 38, 11, 11, 1, 1, 1] 53 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 148 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: REAL300000220751 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC3=C2OC(F)(F)O3)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 2, 2, 2, 3, 3, 1, 11, 11, 38, 38, 38] 53 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 82 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220751 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220751 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220751/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220751 Building REAL300000220752 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220752' /scratch/stefan/7769890/working/building/REAL300000220752 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220752 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220752/0 /scratch/stefan/7769890/working/building/REAL300000220752 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/764 `/scratch/stefan/7769890/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(N(C)C)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220752 none CC1=CC(N(C)C)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [44, 44, 44, 12, 15, 52, 51, 44, 44, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 44, 44, 44, 44, 53, 53, 52, 54, 52, 53, 44, 44, 13, 12, 3, 3, 2, 2, 2, 1] 72 rigid atoms, others: [43, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 265 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: REAL300000220752 none CC1=CC(N(C)C)=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 7, 7, 1, 1, 1, 1, 9, 9, 44, 44, 44, 44, 44, 66, 66, 66, 44, 44, 44, 2, 2, 2, 1, 7, 7, 7, 7, 7, 7, 1, 1, 9, 9, 66, 66, 44, 44, 44, 44] 72 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 34, 35, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 214 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220752 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220752 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220752/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220752 Building REAL300000220753 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220753' /scratch/stefan/7769890/working/building/REAL300000220753 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220753 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220753/0 /scratch/stefan/7769890/working/building/REAL300000220753 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/765 `/scratch/stefan/7769890/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(S(C)(=O)=O)=C2)=N1) `REAL300000220753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220753 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(S(C)(=O)=O)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 45, 48, 48, 27, 27, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 27, 27, 27, 27, 45, 45, 27, 5, 5, 1, 1, 1, 3, 3, 3, 1] 65 rigid atoms, others: [32, 33, 34, 38, 12, 13, 14, 15, 16, 17, 18, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 169 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: REAL300000220753 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(S(C)(=O)=O)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 27, 27, 9, 27, 27, 41, 41, 41, 27, 1, 2, 2, 2, 3, 3, 1, 9, 9, 27, 27, 16, 41, 41, 41, 27] 65 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 197 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220753 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220753 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220753/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220753 Building REAL300000220754 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220754' /scratch/stefan/7769890/working/building/REAL300000220754 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220754 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220754/0 /scratch/stefan/7769890/working/building/REAL300000220754 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/766 `/scratch/stefan/7769890/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2C2CCCC2)=N1) `REAL300000220754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220754 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2C2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 129, 159, 159, 79, 79, 79, 10, 10, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 79, 79, 79, 79, 129, 129, 79, 10, 10, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 535 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220754 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2C2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 79, 79, 79, 79, 79, 153, 153, 153, 153, 1, 2, 2, 2, 3, 3, 1, 12, 12, 79, 79, 153, 153, 153, 153, 153, 153, 153, 153, 153] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 372 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220754 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2C2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 153, 153, 153, 201, 201, 201, 153, 153, 153, 44, 44, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 201, 201, 153, 44, 44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22] set([0, 1, 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]) total number of confs: 527 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220754 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220754 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220754/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220754 Building REAL300000220755 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220755' /scratch/stefan/7769890/working/building/REAL300000220755 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220755 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220755/0 /scratch/stefan/7769890/working/building/REAL300000220755 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/767 `/scratch/stefan/7769890/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C3OCCCCOC3=C2)=N1) `REAL300000220755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220755 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C3OCCCCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 33, 33, 33, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 33, 33, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 32, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 111 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220755 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C3OCCCCOC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 1, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 57 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220755 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220755 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220755/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220755 Building REAL300000220756 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220756' /scratch/stefan/7769890/working/building/REAL300000220756 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220756 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220756/0 /scratch/stefan/7769890/working/building/REAL300000220756 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/768 `/scratch/stefan/7769890/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=CC(Br)=C2)=N1) `REAL300000220756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220756 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=CC(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [23, 23, 23, 23, 33, 33, 33, 23, 23, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 33, 33, 23, 6, 6, 1, 1, 1] 33 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 95 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220756 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=CC(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23, 21, 23, 23, 23, 1, 2, 2, 2, 3, 3, 1, 10, 10, 23, 21, 23] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 67 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220756 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220756 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220756/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220756 Building REAL300000220757 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220757' /scratch/stefan/7769890/working/building/REAL300000220757 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220757 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220757/0 /scratch/stefan/7769890/working/building/REAL300000220757 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/769 `/scratch/stefan/7769890/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220757 none COC1=CC(F)=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [43, 24, 24, 24, 24, 24, 24, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 24, 43, 43, 43, 24, 24, 11, 11, 3, 3, 2, 2, 2, 1, 24] 63 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 104 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: REAL300000220757 none COC1=CC(F)=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 41, 54, 54, 24, 24, 24, 1, 3, 3, 3, 1, 1, 6, 6, 41, 41, 24, 24, 24, 24, 1] 63 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 22, 36, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220757 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220757 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220757/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220757 Building REAL300000220758 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220758' /scratch/stefan/7769890/working/building/REAL300000220758 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220758 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220758/0 /scratch/stefan/7769890/working/building/REAL300000220758 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/770 `/scratch/stefan/7769890/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC(C)C)N1) `REAL300000220758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220758 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 72, 93, 93, 39, 39, 39, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 23, 29, 39, 39, 39, 39, 72, 72, 9, 9, 1, 1, 1, 1, 18, 18, 29, 29, 29, 29, 29, 29, 29, 39] 201 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 489 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220758 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OCC(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 8, 8, 39, 39, 17, 39, 39, 39, 95, 138, 145, 153, 1, 2, 2, 2, 3, 3, 8, 8, 39, 39, 39, 39, 138, 138, 153, 153, 153, 153, 153, 153, 153, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 45, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 603 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220758 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220758 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220758/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220758 Building REAL300000220759 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220759' /scratch/stefan/7769890/working/building/REAL300000220759 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220759 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220759/0 /scratch/stefan/7769890/working/building/REAL300000220759 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/771 `/scratch/stefan/7769890/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC(=O)CC) `REAL300000220759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220759 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC(=O)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 19, 19, 19, 19, 47, 90, 90, 141, 56, 56, 56, 56, 56, 19, 5, 5, 2, 2, 2, 3, 3, 1, 19, 19, 141, 141, 141, 141, 141] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 571 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220759 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1OC(=O)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 12, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 19, 34, 49, 49, 19, 19, 19, 1, 1, 1, 1, 7, 16, 16, 39, 8, 8, 8, 8, 8, 1, 5, 5, 19, 19, 19, 34, 34, 19, 1, 1, 39, 39, 39, 39, 39] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 42, 43, 20, 21, 22, 23] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 319 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220759 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220759 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220759/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220759 Building REAL300000220760 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220760' /scratch/stefan/7769890/working/building/REAL300000220760 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220760 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220760/0 /scratch/stefan/7769890/working/building/REAL300000220760 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/772 `/scratch/stefan/7769890/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(C)(=O)=O)S2)=N1) `REAL300000220760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220760 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(C)(=O)=O)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [57, 57, 57, 57, 87, 89, 89, 57, 57, 57, 11, 11, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1, 57, 57, 57, 57, 87, 87, 57, 11, 11, 1, 1, 7, 7, 7] 108 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 292 number of broken/clashed sets: 107 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220760 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(C)(=O)=O)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 57, 57, 57, 57, 86, 86, 86, 57, 1, 2, 2, 2, 3, 3, 1, 11, 11, 57, 57, 86, 86, 86] 108 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 267 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220760 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220760 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220760/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220760 Building REAL300000220761 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220761' /scratch/stefan/7769890/working/building/REAL300000220761 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220761 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220761/0 /scratch/stefan/7769890/working/building/REAL300000220761 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/773 `/scratch/stefan/7769890/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1C(F)(F)F) `REAL300000220761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220761 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 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: [17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 17, 17, 7, 7, 17, 17, 17, 17, 17, 17, 17, 7, 7, 2, 2, 2, 3, 3, 1, 17, 17] 32 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 128 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: REAL300000220761 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 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, 7, 7, 17, 17, 17, 17, 17, 32, 32, 32, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 7, 7, 17, 17, 17, 32, 32, 17, 1, 1] 32 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 18, 19, 20, 21, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 133 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220761 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220761 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220761/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220761 Building REAL300000220762 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220762' /scratch/stefan/7769890/working/building/REAL300000220762 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220762 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220762/0 /scratch/stefan/7769890/working/building/REAL300000220762 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/774 `/scratch/stefan/7769890/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(C)(=O)=O)O2)=N1) `REAL300000220762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220762 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(C)(=O)=O)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [64, 63, 64, 64, 94, 101, 101, 64, 64, 64, 13, 13, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1, 63, 64, 64, 64, 94, 94, 64, 13, 13, 1, 1, 7, 7, 7] 117 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 325 number of broken/clashed sets: 116 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220762 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(C)(=O)=O)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 64, 64, 64, 64, 89, 89, 89, 64, 1, 2, 2, 2, 3, 3, 1, 11, 11, 64, 64, 89, 89, 89] 117 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 252 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220762 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220762 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220762/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220762 Building REAL300000220763 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220763' /scratch/stefan/7769890/working/building/REAL300000220763 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220763 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220763/0 /scratch/stefan/7769890/working/building/REAL300000220763 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/775 `/scratch/stefan/7769890/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3CC3)=C2)N1) `REAL300000220763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220763 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3CC3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 55, 90, 90, 34, 34, 34, 7, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 1, 34, 34, 34, 34, 55, 55, 7, 7, 1, 1, 1, 9, 9, 9, 9, 9, 1, 34] 126 rigid atoms, others: [32, 38, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 39]) total number of confs: 317 number of broken/clashed sets: 126 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220763 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3CC3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 34, 34, 12, 34, 34, 89, 89, 34, 1, 2, 2, 2, 3, 3, 12, 12, 34, 34, 12, 89, 89, 89, 89, 89, 34, 1] 126 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 280 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220763 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3CC3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 126, 126, 126, 89, 89, 89, 30, 30, 9, 9, 9, 9, 9, 1, 1, 1, 1, 9, 89, 89, 89, 89, 126, 126, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 9, 89] 126 rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 364 number of broken/clashed sets: 126 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220763 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220763 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220763/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220763 Building REAL300000220764 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220764' /scratch/stefan/7769890/working/building/REAL300000220764 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220764 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220764/0 /scratch/stefan/7769890/working/building/REAL300000220764 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/776 `/scratch/stefan/7769890/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NSC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220764 none COC1=NSC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [59, 41, 41, 41, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 41, 59, 59, 59, 11, 11, 2, 2, 2, 3, 3, 1, 41] 77 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32]) total number of confs: 122 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220764 none COC1=NSC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 41, 41, 41, 41, 41, 55, 59, 59, 41, 41, 41, 1, 3, 3, 3, 12, 12, 41, 41, 41, 55, 55, 41, 1] 77 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 20] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 167 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220764 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220764 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220764/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220764 Building REAL300000220765 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220765' /scratch/stefan/7769890/working/building/REAL300000220765 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220765 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220765/0 /scratch/stefan/7769890/working/building/REAL300000220765 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/777 `/scratch/stefan/7769890/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3NC(=O)NC3=C2)N1) `REAL300000220765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220765 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3NC(=O)NC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 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: [19, 19, 19, 19, 27, 27, 27, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 27, 27, 6, 6, 1, 1, 1, 1, 1, 19] 27 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 79 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: REAL300000220765 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3NC(=O)NC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 9, 9, 19, 19, 19, 19, 19, 1] 27 rigid atoms, others: [0, 1, 2, 3, 36, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 61 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220765 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220765 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220765/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220765 Building REAL300000220766 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220766' /scratch/stefan/7769890/working/building/REAL300000220766 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220766 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220766/0 /scratch/stefan/7769890/working/building/REAL300000220766 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/778 `/scratch/stefan/7769890/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C#N)C(F)=C2)N1) `REAL300000220766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) Killed Solvation calculation failed Skipping REAL300000220766 0 /scratch/stefan/7769890/working/building/REAL300000220766 /scratch/stefan/7769890/working /scratch/stefan/7769890 `0' -> `0.failed' Finished preparing REAL300000220766 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Found failed protomers Marking REAL300000220766 as failed `/scratch/stefan/7769890/working/building/REAL300000220766' -> `/scratch/stefan/7769890/failed/REAL300000220766' Building REAL300000220767 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220767' /scratch/stefan/7769890/working/building/REAL300000220767 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220767 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220767/0 /scratch/stefan/7769890/working/building/REAL300000220767 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/779 `/scratch/stefan/7769890/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C3OC(F)(F)OC3=C2)=N1) `REAL300000220767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220767 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C3OC(F)(F)OC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 29, 29, 29, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 29, 29, 20, 6, 6, 1, 1, 1] 29 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220767 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C3OC(F)(F)OC3=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 3, 1, 9, 9, 20, 20, 20] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 62 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220767 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220767 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220767/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220767 Building REAL300000220768 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220768' /scratch/stefan/7769890/working/building/REAL300000220768 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220768 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220768/0 /scratch/stefan/7769890/working/building/REAL300000220768 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/780 `/scratch/stefan/7769890/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(F)=C1) `REAL300000220768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220768 none CC1=CC(F)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [9, 9, 14, 14, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 9, 9, 3, 3, 1, 1, 1, 1, 14] 22 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) 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: REAL300000220768 none CC1=CC(F)=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 22, 22, 22, 14, 14, 14, 1, 1, 1, 2, 2, 2, 1, 6, 6, 22, 22, 14, 14, 14, 14, 1] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220768 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220768 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220768/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220768 Building REAL300000220769 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220769' /scratch/stefan/7769890/working/building/REAL300000220769 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220769 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220769/0 /scratch/stefan/7769890/working/building/REAL300000220769 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/781 `/scratch/stefan/7769890/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C(=O)N(C)C)N1) `REAL300000220769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220769 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C(=O)N(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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] 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: [42, 42, 42, 42, 54, 60, 60, 42, 42, 42, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 42, 42, 42, 42, 54, 54, 9, 9, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 39] 78 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 181 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220769 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C(=O)N(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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] 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 42, 42, 42, 42, 42, 42, 66, 66, 67, 67, 1, 2, 2, 2, 3, 3, 11, 11, 42, 42, 42, 42, 67, 67, 67, 67, 67, 67, 1] 78 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 42] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 183 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220769 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220769 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220769/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220769 Building REAL300000220770 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220770' /scratch/stefan/7769890/working/building/REAL300000220770 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220770 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220770/0 /scratch/stefan/7769890/working/building/REAL300000220770 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/782 `/scratch/stefan/7769890/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=CC=N2)N1) `REAL300000220770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220770 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=CC=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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: [47, 47, 47, 47, 79, 79, 79, 47, 47, 47, 9, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 47, 47, 47, 47, 79, 79, 9, 9, 1, 1, 4, 4, 4, 4, 47] 79 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 261 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220770 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=CC=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 47, 47, 47, 47, 47, 48, 48, 48, 48, 48, 1, 2, 2, 2, 3, 3, 11, 11, 47, 47, 48, 48, 48, 48, 1] 79 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220770 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=CC=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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, 48, 48, 48, 79, 79, 79, 48, 48, 48, 15, 15, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 79, 79, 15, 15, 4, 4, 1, 1, 1, 1, 48] 79 rigid atoms, others: [34, 35, 36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 265 number of broken/clashed sets: 78 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220770 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220770 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220770/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220770 Building REAL300000220771 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220771' /scratch/stefan/7769890/working/building/REAL300000220771 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220771 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220771/0 /scratch/stefan/7769890/working/building/REAL300000220771 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/783 `/scratch/stefan/7769890/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NN(C)C=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)O1) `REAL300000220771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220771 none CC1=CC=C(C2=NN(C)C=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 52, 52, 52, 52, 52, 91, 138, 138, 52, 53, 52, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 11, 11, 91, 91, 53, 53, 53, 52] 201 rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 512 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220771 none CC1=CC=C(C2=NN(C)C=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 52, 52, 137, 137, 137, 137, 137, 201, 201, 201, 137, 137, 137, 1, 2, 2, 2, 1, 1, 12, 12, 12, 12, 52, 52, 201, 201, 137, 137, 137, 137] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220771 none CC1=CC=C(C2=NN(C)C=C2C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [137, 137, 137, 137, 53, 52, 52, 52, 52, 52, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 137, 137, 137, 137, 137, 137, 53, 53, 53, 52, 9, 9, 3, 3, 2, 2, 2, 1] 201 rigid atoms, others: [42, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 221 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220771 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220771 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220771/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220771 Building REAL300000220772 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220772' /scratch/stefan/7769890/working/building/REAL300000220772 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220772 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220772/0 /scratch/stefan/7769890/working/building/REAL300000220772 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/784 `/scratch/stefan/7769890/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2CC(C)C)N1) `REAL300000220772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220772 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2CC(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 120, 155, 155, 72, 72, 72, 10, 10, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 72, 72, 72, 72, 120, 120, 10, 10, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 72] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 550 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220772 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2CC(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 72, 72, 72, 72, 72, 111, 129, 129, 1, 2, 2, 2, 3, 3, 12, 12, 72, 72, 111, 111, 129, 129, 129, 129, 129, 129, 129, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 41] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 439 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220772 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220772 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220772/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220772 Building REAL300000220773 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220773' /scratch/stefan/7769890/working/building/REAL300000220773 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220773 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220773/0 /scratch/stefan/7769890/working/building/REAL300000220773 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/785 `/scratch/stefan/7769890/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CN=C2Cl)=N1) `REAL300000220773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220773 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CN=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [39, 39, 39, 39, 45, 45, 45, 39, 39, 39, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 45, 45, 39, 7, 7, 1, 1] 45 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 89 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: REAL300000220773 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CN=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 3, 3, 1, 12, 12, 39, 39] 45 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220773 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220773 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220773/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220773 Building REAL300000220774 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220774' /scratch/stefan/7769890/working/building/REAL300000220774 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220774 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220774/0 /scratch/stefan/7769890/working/building/REAL300000220774 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/786 `/scratch/stefan/7769890/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=NNC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220774 none CCOC(=O)C1=NNC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 135, 133, 67, 133, 67, 67, 67, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 67, 156, 156, 156, 156, 156, 67, 11, 11, 2, 2, 2, 3, 3, 1, 67] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 456 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220774 none CCOC(=O)C1=NNC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 6, 1, 6, 1, 1, 1, 1, 1, 13, 13, 67, 67, 67, 67, 67, 106, 134, 134, 67, 67, 67, 1, 20, 20, 20, 19, 19, 1, 13, 13, 67, 67, 67, 106, 106, 62, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 23, 38, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 516 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220774 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220774 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220774/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220774 Building REAL300000220775 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220775' /scratch/stefan/7769890/working/building/REAL300000220775 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220775 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220775/0 /scratch/stefan/7769890/working/building/REAL300000220775 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/787 `/scratch/stefan/7769890/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CN1) `REAL300000220775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220775 none COC(=O)C1=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 4, 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: [115, 115, 55, 115, 55, 55, 55, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 55, 55, 115, 115, 115, 55, 55, 55, 11, 11, 3, 3, 2, 2, 2, 1, 55, 55] 151 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220775 none COC(=O)C1=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 4, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 9, 9, 55, 55, 55, 55, 55, 83, 95, 95, 55, 55, 55, 1, 1, 13, 13, 13, 2, 2, 2, 9, 9, 83, 83, 55, 55, 55, 55, 1, 1] 151 rigid atoms, others: [2, 4, 5, 6, 7, 8, 39, 22, 23, 38] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220775 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220775 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220775/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220775 Building REAL300000220776 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220776' /scratch/stefan/7769890/working/building/REAL300000220776 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220776 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220776/0 /scratch/stefan/7769890/working/building/REAL300000220776 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/788 `/scratch/stefan/7769890/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C=CC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1) `REAL300000220776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220776 none COC(=O)C=CC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [158, 158, 114, 157, 114, 61, 61, 61, 61, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 61, 158, 158, 158, 114, 114, 61, 61, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 422 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220776 none COC(=O)C=CC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 10, 37, 10, 1, 1, 1, 1, 1, 1, 12, 12, 61, 61, 61, 61, 61, 90, 115, 115, 61, 61, 61, 1, 38, 38, 38, 10, 10, 1, 1, 12, 12, 62, 62, 62, 90, 90, 61] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 24, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 452 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220776 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220776 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220776/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220776 Building REAL300000220777 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220777' /scratch/stefan/7769890/working/building/REAL300000220777 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220777 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220777/0 /scratch/stefan/7769890/working/building/REAL300000220777 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/789 `/scratch/stefan/7769890/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)C=C1C) `REAL300000220777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220777 none CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 67, 76, 76, 50, 50, 50, 1, 4, 4, 5, 5, 5, 5, 5, 5, 1, 11, 11, 50, 50, 50, 67, 67, 50, 4, 5, 5, 5] 89 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 240 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220777 none CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 32, 32, 74, 74, 74, 74, 74, 89, 89, 89, 74, 74, 74, 4, 1, 1, 1, 2, 2, 2, 1, 1, 4, 31, 32, 74, 74, 74, 89, 89, 74, 1, 2, 2, 2] 89 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 233 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220777 none CC1=CC=C(C2=NC=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)S2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 74, 74, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 50, 74, 74, 74, 74, 74, 74, 74, 74, 50, 11, 11, 2, 2, 2, 3, 3, 1, 74, 74, 74, 74] 89 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 89 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220777 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220777 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220777/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220777 Building REAL300000220778 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220778' /scratch/stefan/7769890/working/building/REAL300000220778 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220778 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220778/0 /scratch/stefan/7769890/working/building/REAL300000220778 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/790 `/scratch/stefan/7769890/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(C(=O)[O-])C=NN2C)N1) `REAL300000220778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220778 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(C(=O)[O-])C=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 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, 26, 33, 41, 41, 26, 26, 26, 9, 9, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 26, 26, 26, 26, 33, 33, 9, 9, 1, 2, 2, 2, 26] 41 rigid atoms, others: [12, 13, 14, 15, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220778 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(C(=O)[O-])C=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 26, 26, 32, 32, 26, 26, 26, 26, 1, 2, 2, 2, 3, 3, 9, 9, 26, 26, 26, 26, 1] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 91 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220778 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220778 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220778/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220778 Building REAL300000220779 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220779' /scratch/stefan/7769890/working/building/REAL300000220779 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220779 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220779/0 /scratch/stefan/7769890/working/building/REAL300000220779 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/791 `/scratch/stefan/7769890/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(C)(C)C#N)C=C2)N1) `REAL300000220779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) Killed Solvation calculation failed Skipping REAL300000220779 0 /scratch/stefan/7769890/working/building/REAL300000220779 /scratch/stefan/7769890/working /scratch/stefan/7769890 `0' -> `0.failed' Finished preparing REAL300000220779 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Found failed protomers Marking REAL300000220779 as failed `/scratch/stefan/7769890/working/building/REAL300000220779' -> `/scratch/stefan/7769890/failed/REAL300000220779' Building REAL300000220780 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220780' /scratch/stefan/7769890/working/building/REAL300000220780 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220780 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220780/0 /scratch/stefan/7769890/working/building/REAL300000220780 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/792 `/scratch/stefan/7769890/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(C)O1) `REAL300000220780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220780 none COC(=O)C1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 75, 167, 75, 75, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 75, 75, 75, 167, 167, 167, 75, 12, 12, 2, 2, 2, 3, 3, 1, 75, 75, 75] 187 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 400 number of broken/clashed sets: 186 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220780 none COC(=O)C1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 10, 10, 75, 75, 75, 75, 75, 119, 146, 146, 75, 75, 75, 1, 1, 1, 13, 13, 13, 1, 10, 11, 75, 75, 75, 119, 119, 75, 2, 2, 2] 187 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 505 number of broken/clashed sets: 186 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220780 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220780 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220780/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220780 Building REAL300000220781 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220781' /scratch/stefan/7769890/working/building/REAL300000220781 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220781 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220781/0 /scratch/stefan/7769890/working/building/REAL300000220781 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/793 `/scratch/stefan/7769890/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C(C)C)N1) `REAL300000220781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220781 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 31, 31, 44, 44, 44, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 31, 31, 31, 31, 44, 44, 7, 7, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 30] 44 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 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: REAL300000220781 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2C(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 6, 6, 1, 1, 1, 1, 1, 10, 10, 31, 31, 10, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 10, 10, 31, 31, 10, 31, 31, 31, 31, 31, 31, 31, 31, 1] 44 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 41] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 112 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220781 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220781 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220781/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220781 Building REAL300000220782 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220782' /scratch/stefan/7769890/working/building/REAL300000220782 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220782 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220782/0 /scratch/stefan/7769890/working/building/REAL300000220782 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/794 `/scratch/stefan/7769890/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(O)=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220782 none COC1=CC(O)=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [46, 28, 28, 21, 28, 28, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 28, 46, 46, 46, 11, 56, 28, 11, 11, 3, 3, 2, 2, 2, 1, 28] 132 rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 198 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: REAL300000220782 none COC1=CC(O)=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 45, 57, 57, 28, 28, 28, 1, 3, 3, 3, 1, 2, 1, 6, 6, 45, 45, 28, 28, 28, 28, 1] 132 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 22, 26, 28, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 196 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220782 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220782 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220782/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220782 Building REAL300000220783 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220783' /scratch/stefan/7769890/working/building/REAL300000220783 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220783 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220783/0 /scratch/stefan/7769890/working/building/REAL300000220783 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/795 `/scratch/stefan/7769890/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN3CCCCC3=C2)N1) `REAL300000220783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220783 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN3CCCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 29, 29, 29, 18, 18, 18, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 19, 19, 19, 29, 29, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16] 29 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 39]) total number of confs: 106 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: REAL300000220783 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN3CCCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 3, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 58 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220783 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220783 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220783/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220783 Building REAL300000220784 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220784' /scratch/stefan/7769890/working/building/REAL300000220784 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220784 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220784/0 /scratch/stefan/7769890/working/building/REAL300000220784 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/796 `/scratch/stefan/7769890/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=NN2C2=CC=CC=C2)N1) `REAL300000220784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220784 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=NN2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 116, 125, 125, 67, 67, 67, 10, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 67, 67, 67, 67, 116, 116, 10, 10, 1, 6, 6, 2, 6, 6, 67] 132 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 432 number of broken/clashed sets: 131 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220784 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=NN2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 67, 67, 82, 82, 75, 82, 82, 1, 2, 2, 2, 3, 3, 12, 12, 67, 82, 82, 81, 82, 82, 1] 132 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 178 number of broken/clashed sets: 131 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220784 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=NN2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [82, 82, 82, 82, 132, 132, 132, 82, 82, 82, 21, 21, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 132, 132, 21, 21, 6, 1, 1, 1, 1, 1, 82] 132 rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 425 number of broken/clashed sets: 131 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220784 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220784 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220784/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220784 Building REAL300000220785 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220785' /scratch/stefan/7769890/working/building/REAL300000220785 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220785 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220785/0 /scratch/stefan/7769890/working/building/REAL300000220785 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/797 `/scratch/stefan/7769890/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CN=CC=C3O2)N1) `REAL300000220785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220785 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CN=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 4, 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, 27, 27, 37, 37, 37, 27, 27, 27, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 37, 37, 10, 10, 1, 1, 1, 1, 28] 37 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 107 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: REAL300000220785 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CN=CC=C3O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 11, 11, 27, 28, 27, 28, 1] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 79 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220785 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220785 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220785/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220785 Building REAL300000220786 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220786' /scratch/stefan/7769890/working/building/REAL300000220786 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220786 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220786/0 /scratch/stefan/7769890/working/building/REAL300000220786 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/798 `/scratch/stefan/7769890/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1F) `REAL300000220786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220786 none COC1=CC(OC)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 38, 38, 85, 85, 85, 124, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 85, 85, 85, 142, 142, 142, 85, 124, 124, 124, 12, 12, 2, 2, 2, 3, 3, 1, 85] 201 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 447 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220786 none COC1=CC(OC)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 12, 12, 85, 85, 85, 85, 85, 130, 185, 185, 85, 85, 85, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 12, 12, 85, 85, 85, 130, 130, 76, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 40, 22, 23, 24, 28] set([0, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 625 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220786 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220786 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220786/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220786 Building REAL300000220787 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220787' /scratch/stefan/7769890/working/building/REAL300000220787 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220787 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220787/0 /scratch/stefan/7769890/working/building/REAL300000220787 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/799 `/scratch/stefan/7769890/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220787 none COC1=CC(F)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.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, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [124, 72, 72, 72, 72, 72, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 72, 72, 72, 135, 124, 124, 124, 72, 12, 12, 2, 2, 2, 3, 3, 1, 72, 135, 135, 135] 177 rigid atoms, others: [36, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40]) total number of confs: 323 number of broken/clashed sets: 177 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220787 none COC1=CC(F)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.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, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 72, 72, 72, 72, 72, 115, 138, 138, 72, 72, 72, 1, 1, 1, 4, 3, 3, 3, 1, 11, 11, 72, 72, 72, 115, 115, 72, 1, 4, 4, 4] 177 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 28, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 452 number of broken/clashed sets: 177 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220787 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220787 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220787/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220787 Building REAL300000220788 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220788' /scratch/stefan/7769890/working/building/REAL300000220788 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220788 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220788/0 /scratch/stefan/7769890/working/building/REAL300000220788 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/800 `/scratch/stefan/7769890/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(Cl)=C1) `REAL300000220788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220788 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [27, 21, 27, 27, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 3, 3, 2, 2, 2, 1, 27] 33 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 101 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: REAL300000220788 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 9, 9, 27, 27, 27, 27, 27, 33, 33, 33, 27, 27, 27, 1, 1, 1, 2, 2, 2, 1, 1, 9, 9, 33, 33, 27, 27, 27, 26, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220788 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220788 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220788/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220788 Building REAL300000220789 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220789' /scratch/stefan/7769890/working/building/REAL300000220789 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220789 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220789/0 /scratch/stefan/7769890/working/building/REAL300000220789 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/801 `/scratch/stefan/7769890/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(N)(=O)=O)C=C2F)=N1) `REAL300000220789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220789 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(N)(=O)=O)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 39, 41, 41, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 27, 27, 27, 27, 39, 39, 27, 9, 9, 1, 1, 5, 5, 1] 145 rigid atoms, others: [33, 34, 37, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 141 number of broken/clashed sets: 145 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220789 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(S(N)(=O)=O)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 27, 27, 17, 27, 97, 97, 97, 27, 27, 27, 1, 2, 2, 2, 3, 3, 1, 11, 11, 27, 27, 97, 97, 27] 145 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 394 number of broken/clashed sets: 145 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220789 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220789 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220789/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220789 Building REAL300000220790 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220790' /scratch/stefan/7769890/working/building/REAL300000220790 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220790 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220790/0 /scratch/stefan/7769890/working/building/REAL300000220790 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/802 `/scratch/stefan/7769890/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(Cl)C(C#N)=C2)=N1) `REAL300000220790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220790 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(Cl)C(C#N)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.1', 'N.1', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 30, 30, 30, 24, 24, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 30, 30, 24, 6, 6, 1, 1] 30 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 73 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: REAL300000220790 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(Cl)C(C#N)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.1', 'N.1', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 3, 1, 9, 9, 24, 24] 30 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 69 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220790 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220790 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220790/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220790 Building REAL300000220791 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220791' /scratch/stefan/7769890/working/building/REAL300000220791 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220791 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220791/0 /scratch/stefan/7769890/working/building/REAL300000220791 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/803 `/scratch/stefan/7769890/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C=C2F)N1) `REAL300000220791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220791 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [36, 36, 36, 36, 41, 41, 41, 36, 36, 36, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 41, 41, 11, 11, 1, 1, 2, 1, 36] 82 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 31, 33]) total number of confs: 88 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220791 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 36, 36, 11, 36, 36, 36, 36, 1, 2, 2, 2, 3, 3, 10, 10, 36, 36, 72, 36, 1] 82 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 225 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220791 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220791 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220791/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220791 Building REAL300000220792 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220792' /scratch/stefan/7769890/working/building/REAL300000220792 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220792 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220792/0 /scratch/stefan/7769890/working/building/REAL300000220792 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/804 `/scratch/stefan/7769890/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(F)=C1) `REAL300000220792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220792 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [52, 33, 11, 33, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 33, 33, 33, 52, 52, 52, 33, 33, 11, 11, 3, 3, 2, 2, 2, 1, 33] 70 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 188 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: REAL300000220792 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [2, 1, 1, 1, 1, 1, 1, 10, 10, 33, 33, 33, 33, 33, 52, 70, 70, 33, 33, 33, 1, 1, 1, 3, 3, 3, 1, 1, 10, 10, 52, 52, 33, 33, 33, 33, 1] 70 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 245 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220792 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220792 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220792/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220792 Building REAL300000220793 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220793' /scratch/stefan/7769890/working/building/REAL300000220793 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220793 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220793/0 /scratch/stefan/7769890/working/building/REAL300000220793 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/805 `/scratch/stefan/7769890/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2CCC3)N1) `REAL300000220793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220793 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2CCC3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 44, 44, 44, 33, 33, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 44, 44, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30] 44 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 39]) 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: REAL300000220793 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2CCC3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 33, 33, 31, 33, 33, 33, 33, 33, 1, 2, 2, 2, 3, 3, 11, 11, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1] 44 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220793 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220793 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220793/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220793 Building REAL300000220794 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220794' /scratch/stefan/7769890/working/building/REAL300000220794 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220794 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220794/0 /scratch/stefan/7769890/working/building/REAL300000220794 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/806 `/scratch/stefan/7769890/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(F)C=NC=C2Br)=N1) `REAL300000220794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220794 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(F)C=NC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 8, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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: [32, 32, 32, 32, 40, 40, 40, 32, 32, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 40, 40, 32, 9, 9, 1, 1] 40 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 96 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220794 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(F)C=NC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 8, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 32, 32, 32, 22, 32, 32, 32, 1, 2, 2, 2, 3, 3, 1, 12, 12, 32, 32] 40 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 101 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220794 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220794 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220794/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220794 Building REAL300000220795 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220795' /scratch/stefan/7769890/working/building/REAL300000220795 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220795 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220795/0 /scratch/stefan/7769890/working/building/REAL300000220795 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/807 `/scratch/stefan/7769890/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(F)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220795 none COC1=CC=CC(F)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [87, 63, 63, 63, 11, 63, 63, 63, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 87, 87, 87, 63, 62, 63, 11, 11, 3, 3, 2, 2, 2, 1] 103 rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: REAL300000220795 none COC1=CC=CC(F)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 63, 63, 63, 63, 63, 97, 103, 103, 63, 63, 63, 3, 3, 3, 1, 1, 1, 11, 11, 97, 97, 63, 63, 63, 63] 103 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220795 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220795 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220795/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220795 Building REAL300000220796 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220796' /scratch/stefan/7769890/working/building/REAL300000220796 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220796 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220796/0 /scratch/stefan/7769890/working/building/REAL300000220796 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/808 `/scratch/stefan/7769890/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(C)=C1) `REAL300000220796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220796 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 72, 59, 8, 8, 23, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 23, 23, 23, 121, 118, 119, 116, 116, 69, 69, 23, 23, 8, 8, 2, 2, 2, 3, 3, 1, 23, 23, 23, 23] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 504 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220796 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 23, 23, 23, 23, 23, 40, 72, 72, 23, 23, 23, 1, 1, 1, 13, 13, 13, 13, 13, 5, 5, 1, 1, 5, 5, 23, 23, 23, 40, 40, 23, 2, 2, 2, 1] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 45, 22, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 310 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220796 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220796 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220796/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220796 Building REAL300000220797 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220797' /scratch/stefan/7769890/working/building/REAL300000220797 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220797 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220797/0 /scratch/stefan/7769890/working/building/REAL300000220797 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/809 `/scratch/stefan/7769890/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=NC=C3S2)N1) `REAL300000220797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220797 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=NC=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 25, 25, 25, 37, 37, 37, 25, 25, 25, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 26, 26, 26, 37, 37, 11, 11, 1, 1, 1, 1, 25] 37 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 116 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: REAL300000220797 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=NC=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 11, 11, 25, 25, 25, 25, 1] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220797 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220797 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220797/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220797 Building REAL300000220798 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220798' /scratch/stefan/7769890/working/building/REAL300000220798 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220798 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220798/0 /scratch/stefan/7769890/working/building/REAL300000220798 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/810 `/scratch/stefan/7769890/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=CC(Br)=CC=C3O2)=N1) `REAL300000220798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220798 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=CC(Br)=CC=C3O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [27, 27, 27, 27, 35, 35, 35, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 35, 35, 27, 10, 9, 1, 1, 1, 1] 35 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 94 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: REAL300000220798 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC3=CC(Br)=CC=C3O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 1, 9, 9, 27, 27, 27, 27] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 66 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220798 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220798 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220798/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220798 Building REAL300000220799 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220799' /scratch/stefan/7769890/working/building/REAL300000220799 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220799 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220799/0 /scratch/stefan/7769890/working/building/REAL300000220799 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/811 `/scratch/stefan/7769890/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=CC=C1) `REAL300000220799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220799 none CCC1=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [82, 59, 59, 59, 59, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 59, 59, 59, 59, 59, 82, 82, 82, 82, 82, 12, 12, 3, 3, 2, 2, 2, 1, 59, 59, 59, 59] 98 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 244 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: REAL300000220799 none CCC1=C2OC(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 13, 13, 58, 58, 59, 59, 59, 76, 92, 92, 59, 59, 59, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 76, 76, 59, 59, 59, 59, 1, 1, 1, 1] 98 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 41, 20, 21, 22, 23, 24, 38] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 278 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220799 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220799 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220799/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220799 Building REAL300000220800 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220800' /scratch/stefan/7769890/working/building/REAL300000220800 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220800 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220800/0 /scratch/stefan/7769890/working/building/REAL300000220800 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/812 `/scratch/stefan/7769890/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl) `REAL300000220800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220800 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [65, 65, 34, 65, 32, 34, 34, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 34, 34, 34, 65, 65, 65, 34, 34, 11, 11, 2, 2, 2, 3, 3, 1, 34] 89 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 192 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220800 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [7, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 34, 34, 34, 34, 34, 54, 65, 65, 34, 34, 34, 1, 1, 1, 7, 7, 7, 1, 1, 6, 6, 34, 34, 34, 54, 54, 34, 1] 89 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 24, 38, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 224 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220800 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220800 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220800/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220800 Building REAL300000220801 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220801' /scratch/stefan/7769890/working/building/REAL300000220801 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220801 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220801/0 /scratch/stefan/7769890/working/building/REAL300000220801 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/813 `/scratch/stefan/7769890/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCN1C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N=N1) `REAL300000220801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220801 none C=CCCN1C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 136, 107, 40, 40, 40, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 39, 40, 160, 160, 160, 136, 136, 107, 107, 40, 12, 12, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [38, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 640 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220801 none C=CCCN1C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 17, 9, 1, 1, 1, 1, 1, 6, 6, 40, 40, 40, 39, 39, 63, 91, 91, 40, 40, 40, 1, 1, 36, 36, 36, 17, 17, 9, 9, 1, 6, 7, 40, 40, 40, 63, 63, 40] 201 rigid atoms, others: [3, 4, 5, 6, 7, 21, 22, 30] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 446 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220801 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220801 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220801/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220801 Building REAL300000220802 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220802' /scratch/stefan/7769890/working/building/REAL300000220802 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220802 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220802/0 /scratch/stefan/7769890/working/building/REAL300000220802 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/814 `/scratch/stefan/7769890/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN3CCCC3=C2)N1) `REAL300000220802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220802 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN3CCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [21, 21, 21, 21, 28, 28, 28, 20, 21, 20, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 28, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 18] 28 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 86 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: REAL300000220802 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN3CCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 8, 8, 21, 21, 21, 20, 21, 21, 21, 1] 28 rigid atoms, others: [0, 1, 2, 3, 36, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 64 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220802 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220802 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220802/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220802 Building REAL300000220803 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220803' /scratch/stefan/7769890/working/building/REAL300000220803 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220803 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220803/0 /scratch/stefan/7769890/working/building/REAL300000220803 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/815 `/scratch/stefan/7769890/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2CC2CC2)N1) `REAL300000220803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220803 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2CC2CC2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 80, 118, 118, 46, 46, 46, 10, 10, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 46, 46, 46, 46, 80, 80, 10, 10, 1, 1, 7, 7, 19, 19, 19, 19, 19, 46] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 479 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220803 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2CC2CC2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 8, 8, 46, 46, 46, 46, 46, 107, 132, 132, 1, 2, 2, 2, 3, 3, 8, 8, 46, 46, 107, 107, 132, 132, 132, 132, 132, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 463 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220803 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2CC2CC2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 132, 132, 201, 201, 201, 132, 132, 132, 72, 72, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 132, 132, 132, 132, 201, 201, 72, 72, 19, 19, 6, 6, 1, 1, 1, 1, 1, 132] 201 rigid atoms, others: [34, 35, 36, 37, 38, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 675 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220803 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220803 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220803/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220803 Building REAL300000220804 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220804' /scratch/stefan/7769890/working/building/REAL300000220804 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220804 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220804/0 /scratch/stefan/7769890/working/building/REAL300000220804 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/816 `/scratch/stefan/7769890/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3CC3)=C2F)=N1) `REAL300000220804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220804 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3CC3)=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 15, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 76, 120, 120, 45, 45, 45, 9, 9, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 1, 1, 45, 45, 45, 45, 76, 76, 45, 9, 9, 1, 1, 1, 18, 18, 18, 18, 18] 201 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 457 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220804 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3CC3)=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 15, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 45, 45, 45, 45, 45, 107, 147, 147, 45, 45, 1, 2, 2, 2, 3, 3, 1, 11, 11, 45, 45, 45, 147, 147, 147, 147, 147] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 339 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220804 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3CC3)=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 15, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 201, 201, 201, 146, 146, 146, 60, 60, 20, 20, 20, 20, 20, 8, 1, 1, 1, 1, 20, 20, 146, 146, 146, 146, 201, 201, 146, 60, 60, 20, 20, 20, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 576 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220804 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220804 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220804/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220804 Building REAL300000220805 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220805' /scratch/stefan/7769890/working/building/REAL300000220805 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220805 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220805/0 /scratch/stefan/7769890/working/building/REAL300000220805 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/817 `/scratch/stefan/7769890/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C)=C1) `REAL300000220805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220805 none CCOC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 112, 22, 20, 41, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 41, 41, 41, 142, 142, 142, 142, 142, 41, 41, 11, 11, 3, 3, 2, 2, 2, 1, 41, 41, 41, 41] 201 rigid atoms, others: [38, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 421 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: REAL300000220805 none CCOC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 1, 1, 1, 1, 1, 1, 9, 9, 41, 41, 41, 41, 41, 66, 103, 103, 41, 41, 41, 1, 1, 1, 16, 16, 16, 15, 15, 1, 1, 9, 9, 66, 66, 41, 41, 41, 41, 2, 2, 2, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 42, 21, 22, 23, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 415 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220805 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220805 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220805/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220805 Building REAL300000220806 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220806' /scratch/stefan/7769890/working/building/REAL300000220806 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220806 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220806/0 /scratch/stefan/7769890/working/building/REAL300000220806 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/818 `/scratch/stefan/7769890/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(F)=C2OC(F)F)=N1) `REAL300000220806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220806 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(F)=C2OC(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 86, 135, 135, 51, 51, 51, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 51, 51, 51, 51, 86, 86, 51, 9, 9, 1, 1, 1, 23] 201 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 538 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220806 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(F)=C2OC(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 51, 51, 51, 51, 51, 51, 51, 103, 158, 158, 1, 2, 2, 2, 3, 3, 1, 11, 11, 51, 51, 51, 158] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 485 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220806 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220806 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220806/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220806 Building REAL300000220807 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220807' /scratch/stefan/7769890/working/building/REAL300000220807 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220807 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220807/0 /scratch/stefan/7769890/working/building/REAL300000220807 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/819 `/scratch/stefan/7769890/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=CC=C2OC(F)F)=N1) `REAL300000220807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220807 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=CC=C2OC(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 97, 141, 141, 59, 59, 59, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 31, 59, 59, 59, 59, 97, 97, 59, 9, 9, 1, 1, 1, 31] 201 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 578 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220807 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=CC=C2OC(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 59, 59, 59, 38, 59, 59, 59, 139, 186, 186, 1, 2, 2, 2, 3, 3, 1, 11, 11, 59, 59, 59, 186] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 578 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220807 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220807 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220807/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220807 Building REAL300000220808 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220808' /scratch/stefan/7769890/working/building/REAL300000220808 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220808 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220808/0 /scratch/stefan/7769890/working/building/REAL300000220808 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/820 `/scratch/stefan/7769890/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220808 none COC1=CN=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [34, 21, 21, 21, 21, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 21, 34, 34, 34, 21, 21, 10, 10, 3, 3, 2, 2, 2, 1, 21] 61 rigid atoms, others: [34, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: REAL300000220808 none COC1=CN=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 39, 50, 50, 21, 21, 21, 1, 3, 3, 3, 1, 1, 6, 6, 39, 39, 21, 21, 21, 21, 1] 61 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 21, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220808 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220808 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220808/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220808 Building REAL300000220809 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220809' /scratch/stefan/7769890/working/building/REAL300000220809 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220809 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220809/0 /scratch/stefan/7769890/working/building/REAL300000220809 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/821 `/scratch/stefan/7769890/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220809 none COC1=NC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [61, 53, 53, 53, 53, 53, 53, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 61, 61, 61, 53, 53, 53, 12, 12, 3, 3, 2, 2, 2, 1] 69 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 121 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: REAL300000220809 none COC1=NC=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 53, 53, 53, 53, 53, 69, 69, 69, 53, 53, 53, 4, 4, 4, 1, 1, 1, 11, 11, 69, 69, 53, 53, 53, 53] 69 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220809 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220809 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220809/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220809 Building REAL300000220810 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220810' /scratch/stefan/7769890/working/building/REAL300000220810 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220810 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220810/0 /scratch/stefan/7769890/working/building/REAL300000220810 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/822 `/scratch/stefan/7769890/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(O)=C2F)N1) `REAL300000220810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220810 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(O)=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [38, 38, 38, 38, 43, 43, 43, 38, 38, 38, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 43, 43, 11, 11, 1, 1, 1, 2, 38] 86 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 89 number of broken/clashed sets: 86 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220810 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(O)=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 38, 38, 38, 38, 38, 38, 38, 1, 2, 2, 2, 3, 3, 11, 11, 38, 38, 38, 76, 1] 86 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 160 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220810 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220810 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220810/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220810 Building REAL300000220811 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220811' /scratch/stefan/7769890/working/building/REAL300000220811 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220811 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220811/0 /scratch/stefan/7769890/working/building/REAL300000220811 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/823 `/scratch/stefan/7769890/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3CCCC3)=C2)N1) `REAL300000220811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220811 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3CCCC3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 61, 66, 66, 39, 39, 39, 7, 7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 39, 39, 39, 39, 61, 61, 7, 7, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 39] 157 rigid atoms, others: [32, 33, 34, 44, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45]) total number of confs: 221 number of broken/clashed sets: 157 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220811 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3CCCC3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 39, 39, 23, 39, 39, 107, 107, 107, 107, 39, 1, 2, 2, 2, 3, 3, 12, 12, 39, 39, 33, 107, 107, 107, 107, 107, 107, 107, 107, 107, 39, 1] 157 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 45, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 336 number of broken/clashed sets: 157 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220811 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3CCCC3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 157, 157, 157, 107, 107, 107, 28, 28, 8, 8, 7, 8, 8, 1, 1, 1, 1, 1, 1, 8, 107, 107, 107, 107, 157, 157, 28, 28, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 107] 157 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 22] set([0, 1, 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, 44, 45]) total number of confs: 465 number of broken/clashed sets: 157 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220811 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220811 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220811/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220811 Building REAL300000220812 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220812' /scratch/stefan/7769890/working/building/REAL300000220812 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220812 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220812/0 /scratch/stefan/7769890/working/building/REAL300000220812 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/824 `/scratch/stefan/7769890/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)[O-])C(F)=C2)=N1) `REAL300000220812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220812 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)[O-])C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [29, 29, 29, 29, 44, 50, 50, 29, 29, 29, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 29, 29, 29, 29, 44, 44, 29, 6, 6, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 162 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: REAL300000220812 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)[O-])C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 29, 29, 29, 29, 39, 39, 29, 29, 29, 1, 2, 2, 2, 3, 3, 1, 11, 11, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 115 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220812 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220812 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220812/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220812 Building REAL300000220813 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220813' /scratch/stefan/7769890/working/building/REAL300000220813 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220813 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220813/0 /scratch/stefan/7769890/working/building/REAL300000220813 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/825 `/scratch/stefan/7769890/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1F) `REAL300000220813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220813 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [88, 88, 34, 88, 34, 34, 34, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 34, 34, 34, 88, 88, 88, 34, 34, 10, 10, 2, 2, 2, 3, 3, 1, 34] 121 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 241 number of broken/clashed sets: 121 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220813 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 5, 5, 34, 34, 34, 34, 34, 61, 77, 77, 34, 34, 34, 1, 1, 1, 12, 12, 12, 1, 1, 5, 5, 34, 34, 34, 61, 61, 34, 1] 121 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 24, 38, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 294 number of broken/clashed sets: 121 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220813 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220813 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220813/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220813 Building REAL300000220814 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220814' /scratch/stefan/7769890/working/building/REAL300000220814 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220814 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220814/0 /scratch/stefan/7769890/working/building/REAL300000220814 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/826 `/scratch/stefan/7769890/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CN(C)N=C2)N1) `REAL300000220814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220814 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CN(C)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 70, 109, 154, 154, 69, 70, 69, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 70, 70, 70, 70, 109, 109, 12, 12, 1, 2, 2, 2, 12, 12, 12, 12, 12, 70] 201 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 527 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220814 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CN(C)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 70, 70, 70, 70, 70, 70, 148, 148, 148, 148, 148, 1, 2, 2, 2, 3, 3, 11, 11, 70, 70, 70, 70, 148, 148, 148, 148, 148, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 42] set([4, 5, 6, 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, 39, 40, 41]) total number of confs: 243 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220814 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CN(C)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 201, 201, 201, 148, 148, 148, 50, 50, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 201, 201, 50, 50, 12, 12, 12, 12, 1, 2, 2, 2, 1, 148] 201 rigid atoms, others: [37, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 42]) total number of confs: 566 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220814 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220814 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220814/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220814 Building REAL300000220815 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220815' /scratch/stefan/7769890/working/building/REAL300000220815 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220815 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220815/0 /scratch/stefan/7769890/working/building/REAL300000220815 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/827 `/scratch/stefan/7769890/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CSC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1) `REAL300000220815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220815 none COCC1=CSC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 14, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 133, 47, 47, 47, 47, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 47, 158, 158, 158, 133, 133, 47, 9, 9, 2, 2, 2, 3, 3, 1, 47] 201 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 508 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220815 none COCC1=CSC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 14, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 10, 10, 47, 47, 47, 47, 47, 80, 126, 126, 47, 47, 47, 1, 16, 16, 16, 6, 6, 1, 10, 10, 47, 47, 47, 80, 80, 47, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 21, 36, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 483 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220815 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220815 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220815/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220815 Building REAL300000220816 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220816' /scratch/stefan/7769890/working/building/REAL300000220816 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220816 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220816/0 /scratch/stefan/7769890/working/building/REAL300000220816 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/828 `/scratch/stefan/7769890/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C=CC(=O)[O-])O2)=N1) `REAL300000220816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220816 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C=CC(=O)[O-])O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [60, 59, 60, 60, 93, 132, 132, 60, 60, 60, 13, 13, 1, 1, 1, 1, 1, 1, 11, 11, 30, 30, 1, 59, 60, 60, 60, 93, 93, 60, 13, 13, 1, 1, 11, 11] 198 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 521 number of broken/clashed sets: 197 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220816 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C=CC(=O)[O-])O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 60, 60, 60, 60, 145, 145, 162, 162, 60, 1, 2, 2, 2, 3, 3, 1, 11, 11, 60, 60, 145, 145] 198 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 414 number of broken/clashed sets: 197 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220816 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220816 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220816/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220816 Building REAL300000220817 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220817' /scratch/stefan/7769890/working/building/REAL300000220817 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220817 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220817/0 /scratch/stefan/7769890/working/building/REAL300000220817 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/829 `/scratch/stefan/7769890/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3CCC3)N=N2)=N1) `REAL300000220817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220817 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3CCC3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 8, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 95, 123, 123, 71, 71, 71, 11, 11, 1, 1, 1, 1, 1, 13, 13, 13, 1, 1, 71, 71, 71, 71, 95, 95, 71, 12, 11, 1, 13, 13, 13, 13, 13, 13, 13] 178 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 378 number of broken/clashed sets: 177 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220817 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3CCC3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 8, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 71, 71, 71, 143, 143, 143, 71, 71, 1, 2, 2, 2, 3, 3, 1, 11, 11, 71, 143, 143, 143, 143, 143, 143, 143] 178 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 332 number of broken/clashed sets: 177 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220817 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3CCC3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 8, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [143, 143, 143, 143, 178, 178, 178, 143, 143, 143, 74, 74, 13, 13, 13, 1, 1, 1, 1, 1, 13, 13, 143, 143, 143, 143, 178, 178, 143, 74, 74, 13, 1, 1, 1, 1, 1, 1, 1] 178 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 475 number of broken/clashed sets: 177 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220817 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220817 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220817/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220817 Building REAL300000220818 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220818' /scratch/stefan/7769890/working/building/REAL300000220818 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220818 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220818/0 /scratch/stefan/7769890/working/building/REAL300000220818 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/830 `/scratch/stefan/7769890/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)=N1) `REAL300000220818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220818 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 63, 94, 94, 39, 39, 39, 6, 6, 1, 1, 1, 1, 1, 1, 8, 14, 14, 10, 14, 14, 14, 1, 1, 39, 39, 39, 39, 63, 63, 39, 6, 6, 1, 1, 14, 14, 14, 14, 1] 201 rigid atoms, others: [36, 37, 42, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 352 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220818 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 39, 39, 39, 39, 136, 146, 146, 140, 146, 146, 146, 39, 39, 1, 2, 2, 2, 3, 3, 1, 12, 12, 39, 39, 146, 146, 146, 146, 39] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 263 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220818 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 201, 201, 201, 146, 146, 146, 44, 44, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 146, 146, 146, 146, 201, 201, 146, 44, 44, 14, 14, 1, 1, 1, 1, 14] 201 rigid atoms, others: [38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 569 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220818 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220818 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220818/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220818 Building REAL300000220819 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220819' /scratch/stefan/7769890/working/building/REAL300000220819 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220819 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220819/0 /scratch/stefan/7769890/working/building/REAL300000220819 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/831 `/scratch/stefan/7769890/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CC(Cl)=C3)S2)=N1) `REAL300000220819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220819 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CC(Cl)=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [54, 54, 54, 54, 71, 77, 77, 54, 54, 54, 12, 12, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 5, 1, 54, 54, 54, 54, 71, 71, 54, 12, 12, 1, 5, 5, 4, 5] 91 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 216 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: REAL300000220819 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CC(Cl)=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 54, 54, 54, 54, 74, 74, 69, 74, 74, 74, 54, 1, 2, 2, 2, 3, 3, 1, 11, 11, 54, 74, 74, 74, 74] 91 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 161 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220819 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(C3=CC=CC(Cl)=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [74, 74, 74, 74, 91, 91, 91, 74, 74, 74, 32, 32, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 74, 74, 74, 74, 91, 91, 74, 32, 32, 5, 1, 1, 1, 1] 91 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 230 number of broken/clashed sets: 90 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220819 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220819 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220819/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220819 Building REAL300000220820 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220820' /scratch/stefan/7769890/working/building/REAL300000220820 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220820 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220820/0 /scratch/stefan/7769890/working/building/REAL300000220820 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/832 `/scratch/stefan/7769890/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=C(O)C=CC=C3S2)N1) `REAL300000220820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220820 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=C(O)C=CC=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [34, 34, 34, 34, 43, 43, 43, 33, 34, 33, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 43, 43, 12, 12, 1, 2, 1, 1, 1, 34] 86 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 32, 36]) total number of confs: 117 number of broken/clashed sets: 84 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220820 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=C(O)C=CC=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 34, 34, 34, 34, 34, 33, 34, 34, 34, 1, 2, 2, 2, 3, 3, 11, 11, 34, 68, 34, 34, 34, 1] 86 rigid atoms, others: [0, 1, 2, 3, 36, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 153 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220820 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220820 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220820/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220820 Building REAL300000220821 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220821' /scratch/stefan/7769890/working/building/REAL300000220821 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220821 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220821/0 /scratch/stefan/7769890/working/building/REAL300000220821 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/833 `/scratch/stefan/7769890/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C(F)(F)F)=C2)=N1) `REAL300000220821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220821 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [21, 21, 21, 21, 33, 33, 33, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 21, 21, 21, 21, 33, 33, 21, 6, 6, 1, 1] 33 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 112 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: REAL300000220821 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C(F)(F)F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 7, 7, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 7, 7, 21, 21] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 62 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220821 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220821 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220821/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220821 Building REAL300000220822 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220822' /scratch/stefan/7769890/working/building/REAL300000220822 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220822 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220822/0 /scratch/stefan/7769890/working/building/REAL300000220822 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/834 `/scratch/stefan/7769890/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)O2)=N1) `REAL300000220822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220822 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 39, 39, 39, 33, 33, 33, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 33, 33, 33, 33, 39, 39, 33, 13, 13, 1, 1] 39 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 95 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: REAL300000220822 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 33, 33, 33, 33, 33, 33, 33, 33, 1, 2, 2, 2, 3, 3, 1, 11, 11, 33, 33] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 76 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220822 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220822 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220822/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220822 Building REAL300000220823 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220823' /scratch/stefan/7769890/working/building/REAL300000220823 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220823 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220823/0 /scratch/stefan/7769890/working/building/REAL300000220823 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/835 `/scratch/stefan/7769890/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=CC(Cl)=C2)N1) `REAL300000220823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220823 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=CC(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [16, 16, 16, 16, 28, 28, 28, 16, 16, 16, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 28, 28, 7, 7, 1, 1, 1, 16] 28 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 100 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: REAL300000220823 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=CC(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 3, 3, 9, 9, 16, 16, 16, 1] 28 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 56 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220823 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220823 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220823/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220823 Building REAL300000220824 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220824' /scratch/stefan/7769890/working/building/REAL300000220824 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220824 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220824/0 /scratch/stefan/7769890/working/building/REAL300000220824 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/836 `/scratch/stefan/7769890/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(C(F)(F)F)C=NN2C)=N1) `REAL300000220824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220824 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(C(F)(F)F)C=NN2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 36, 36, 36, 49, 49, 49, 36, 36, 36, 6, 6, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 36, 36, 36, 36, 49, 49, 35, 6, 6, 1, 2, 2, 2] 49 rigid atoms, others: [32, 12, 13, 14, 15, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 139 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: REAL300000220824 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(C(F)(F)F)C=NN2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 2, 2, 2, 3, 3, 1, 11, 11, 36, 36, 36, 36] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 82 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220824 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220824 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220824/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220824 Building REAL300000220825 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220825' /scratch/stefan/7769890/working/building/REAL300000220825 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220825 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220825/0 /scratch/stefan/7769890/working/building/REAL300000220825 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/837 `/scratch/stefan/7769890/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(C3CC3)C=NN2C)N1) `REAL300000220825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220825 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(C3CC3)C=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 95, 110, 110, 59, 59, 59, 9, 9, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 59, 59, 59, 59, 95, 95, 9, 9, 8, 8, 8, 8, 8, 1, 2, 2, 2, 59] 148 rigid atoms, others: [35, 12, 13, 14, 15, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 375 number of broken/clashed sets: 147 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220825 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(C3CC3)C=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 59, 59, 99, 99, 59, 59, 59, 59, 1, 2, 2, 2, 3, 3, 12, 12, 99, 99, 99, 99, 99, 59, 59, 59, 59, 1] 148 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 246 number of broken/clashed sets: 147 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220825 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(C3CC3)C=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 148, 148, 148, 101, 101, 101, 31, 31, 8, 8, 1, 1, 1, 1, 8, 8, 8, 8, 101, 101, 101, 101, 148, 148, 31, 31, 1, 1, 1, 1, 1, 8, 9, 9, 9, 101] 148 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39]) total number of confs: 450 number of broken/clashed sets: 147 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220825 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220825 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220825/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220825 Building REAL300000220826 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220826' /scratch/stefan/7769890/working/building/REAL300000220826 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220826 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220826/0 /scratch/stefan/7769890/working/building/REAL300000220826 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/838 `/scratch/stefan/7769890/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(C3CCC3)C=NN2C)N1) `REAL300000220826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220826 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(C3CCC3)C=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 94, 121, 121, 54, 54, 54, 9, 9, 1, 1, 1, 1, 9, 9, 9, 1, 1, 1, 1, 54, 54, 54, 54, 94, 94, 9, 9, 9, 9, 9, 9, 10, 9, 9, 1, 2, 2, 2, 54] 168 rigid atoms, others: [38, 12, 13, 14, 15, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 446 number of broken/clashed sets: 167 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220826 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(C3CCC3)C=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 54, 54, 107, 107, 107, 54, 54, 54, 54, 1, 2, 2, 2, 3, 3, 12, 12, 107, 107, 107, 107, 107, 107, 107, 54, 54, 54, 54, 1] 168 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 42] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 278 number of broken/clashed sets: 167 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220826 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C(C3CCC3)C=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 168, 168, 168, 107, 107, 107, 30, 30, 10, 9, 1, 1, 1, 1, 1, 9, 9, 9, 9, 107, 107, 107, 107, 168, 168, 30, 30, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 107] 168 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42]) total number of confs: 538 number of broken/clashed sets: 167 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220826 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220826 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220826/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220826 Building REAL300000220827 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220827' /scratch/stefan/7769890/working/building/REAL300000220827 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220827 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220827/0 /scratch/stefan/7769890/working/building/REAL300000220827 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/839 `/scratch/stefan/7769890/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(C(F)(F)F)SC=C2)=N1) `REAL300000220827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220827 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(C(F)(F)F)SC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [35, 35, 35, 35, 49, 49, 49, 35, 35, 35, 7, 7, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 35, 35, 35, 35, 49, 49, 32, 7, 7, 1, 1] 49 rigid atoms, others: [32, 12, 13, 14, 15, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 142 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: REAL300000220827 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(C(F)(F)F)SC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 1, 12, 12, 35, 35] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 83 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220827 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220827 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220827/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220827 Building REAL300000220828 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220828' /scratch/stefan/7769890/working/building/REAL300000220828 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220828 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220828/0 /scratch/stefan/7769890/working/building/REAL300000220828 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/840 `/scratch/stefan/7769890/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2C2CCOCC2)=N1) `REAL300000220828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220828 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 123, 159, 159, 71, 71, 71, 10, 10, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 71, 71, 71, 71, 123, 123, 71, 10, 10, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] 184 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 561 number of broken/clashed sets: 183 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220828 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 71, 71, 71, 71, 71, 144, 144, 144, 144, 144, 1, 2, 2, 2, 3, 3, 1, 11, 11, 71, 71, 144, 144, 144, 144, 144, 144, 144, 144, 144] 184 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 365 number of broken/clashed sets: 183 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220828 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2C2CCOCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 144, 184, 184, 184, 144, 144, 144, 40, 40, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 184, 184, 144, 40, 40, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 184 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 462 number of broken/clashed sets: 183 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220828 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220828 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220828/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220828 Building REAL300000220829 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220829' /scratch/stefan/7769890/working/building/REAL300000220829 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220829 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220829/0 /scratch/stefan/7769890/working/building/REAL300000220829 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/841 `/scratch/stefan/7769890/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(F)C=CC(F)=C2Cl)=N1) `REAL300000220829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220829 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(F)C=CC(F)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [33, 33, 33, 33, 41, 41, 41, 33, 33, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 41, 41, 33, 9, 9, 1, 1] 41 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 97 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220829 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(F)C=CC(F)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 1, 2, 2, 2, 3, 3, 1, 12, 12, 33, 33] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 80 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220829 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220829 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220829/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220829 Building REAL300000220830 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220830' /scratch/stefan/7769890/working/building/REAL300000220830 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220830 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220830/0 /scratch/stefan/7769890/working/building/REAL300000220830 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/842 `/scratch/stefan/7769890/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C(OC(C)C)C=C2Cl)=N1) `REAL300000220830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220830 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C(OC(C)C)C=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 64, 100, 140, 140, 64, 64, 64, 9, 9, 1, 1, 1, 1, 1, 1, 1, 10, 21, 21, 1, 1, 1, 64, 64, 64, 64, 100, 100, 64, 9, 9, 1, 21, 21, 21, 21, 21, 21, 21, 1] 201 rigid atoms, others: [34, 42, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 519 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220830 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Cl)=C(OC(C)C)C=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 64, 64, 64, 23, 23, 134, 168, 168, 64, 64, 64, 1, 2, 2, 2, 3, 3, 1, 12, 12, 64, 168, 168, 168, 168, 168, 168, 168, 64] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 522 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220830 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220830 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220830/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220830 Building REAL300000220831 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220831' /scratch/stefan/7769890/working/building/REAL300000220831 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220831 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220831/0 /scratch/stefan/7769890/working/building/REAL300000220831 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/843 `/scratch/stefan/7769890/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3NC=NC3=C2)N1) `REAL300000220831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220831 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3NC=NC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 26, 26, 26, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 26, 26, 6, 6, 1, 1, 1, 1, 1, 22] 26 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 57 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: REAL300000220831 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3NC=NC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 9, 9, 22, 22, 22, 22, 22, 1] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 62 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220831 /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `1' /scratch/stefan/7769890/working/building/REAL300000220831/1 /scratch/stefan/7769890/working/building/REAL300000220831 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 1 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/844 `/scratch/stefan/7769890/working/3D/844' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3N=CNC3=C2)N1) `REAL300000220831.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220831/1/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: REAL300000220831 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3N=CNC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 26, 26, 26, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 26, 26, 6, 6, 1, 1, 1, 1, 1, 22] 26 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 58 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: REAL300000220831 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3N=CNC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 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, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 9, 9, 22, 22, 22, 22, 22, 1] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 64 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220831 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220831 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 1: /scratch/stefan/7769890/working/building/REAL300000220831/1.* 0: /scratch/stefan/7769890/working/building/REAL300000220831/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220831 Building REAL300000220832 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220832' /scratch/stefan/7769890/working/building/REAL300000220832 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220832 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220832/0 /scratch/stefan/7769890/working/building/REAL300000220832 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/845 `/scratch/stefan/7769890/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN(C)C3=CC=CC=C23)N1) `REAL300000220832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220832 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN(C)C3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 32, 42, 42, 42, 32, 32, 32, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 33, 33, 33, 42, 42, 7, 7, 2, 2, 2, 1, 1, 1, 1, 32] 42 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 114 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: REAL300000220832 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=NN(C)C3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 2, 2, 2, 3, 3, 11, 11, 33, 33, 33, 32, 32, 32, 32, 1] 42 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220832 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220832 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220832/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220832 Building REAL300000220833 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220833' /scratch/stefan/7769890/working/building/REAL300000220833 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220833 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220833/0 /scratch/stefan/7769890/working/building/REAL300000220833 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/846 `/scratch/stefan/7769890/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3CCOC3)C=C2)=N1) `REAL300000220833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220833 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3CCOC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 44, 72, 72, 26, 26, 26, 4, 4, 1, 1, 1, 1, 1, 1, 13, 37, 37, 37, 37, 1, 1, 26, 26, 26, 26, 44, 44, 26, 4, 4, 1, 1, 37, 37, 37, 37, 37, 37, 37, 1, 1] 201 rigid atoms, others: [34, 35, 44, 43, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 333 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220833 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3CCOC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 26, 26, 12, 12, 109, 164, 164, 164, 164, 26, 26, 1, 2, 2, 2, 3, 3, 1, 12, 12, 26, 26, 164, 164, 164, 164, 164, 164, 164, 26, 26] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 407 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220833 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC3CCOC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 201, 201, 201, 164, 164, 164, 60, 60, 11, 7, 37, 37, 7, 1, 1, 1, 1, 1, 1, 37, 37, 164, 164, 164, 164, 201, 201, 164, 60, 60, 37, 37, 1, 1, 1, 1, 1, 1, 1, 37, 37] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44]) total number of confs: 576 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220833 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220833 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220833/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220833 Building REAL300000220834 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220834' /scratch/stefan/7769890/working/building/REAL300000220834 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220834 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220834/0 /scratch/stefan/7769890/working/building/REAL300000220834 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/847 `/scratch/stefan/7769890/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=C(N(C)C)C=C2F)=N1) `REAL300000220834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220834 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=C(N(C)C)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 1, 1, 15, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [69, 69, 69, 69, 97, 115, 115, 69, 69, 69, 11, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 1, 69, 69, 69, 69, 97, 97, 69, 11, 11, 1, 7, 7, 7, 7, 7, 7, 1] 115 rigid atoms, others: [33, 40, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 355 number of broken/clashed sets: 115 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220834 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=C(N(C)C)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 1, 1, 15, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 69, 69, 69, 39, 37, 89, 89, 69, 69, 69, 1, 2, 2, 2, 3, 3, 1, 11, 11, 69, 89, 89, 89, 89, 89, 89, 69] 115 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 339 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220834 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220834 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220834/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220834 Building REAL300000220835 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220835' /scratch/stefan/7769890/working/building/REAL300000220835 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220835 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220835/0 /scratch/stefan/7769890/working/building/REAL300000220835 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/848 `/scratch/stefan/7769890/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1) `REAL300000220835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220835 none COC(=O)C1=C(C)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 65, 123, 65, 65, 65, 65, 13, 13, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 64, 123, 123, 123, 65, 65, 65, 65, 13, 13, 2, 2, 2, 3, 3, 1] 145 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 303 number of broken/clashed sets: 144 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220835 none COC(=O)C1=C(C)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 12, 12, 65, 65, 65, 64, 64, 93, 104, 104, 65, 65, 65, 1, 13, 13, 13, 2, 2, 2, 1, 12, 12, 65, 65, 65, 93, 93, 65] 145 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23, 30] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 342 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220835 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220835 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220835/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220835 Building REAL300000220836 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220836' /scratch/stefan/7769890/working/building/REAL300000220836 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220836 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220836/0 /scratch/stefan/7769890/working/building/REAL300000220836 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/849 `/scratch/stefan/7769890/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=NC=C2)N1) `REAL300000220836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220836 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=NC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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: [68, 68, 68, 68, 108, 115, 115, 68, 68, 68, 10, 10, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 68, 68, 68, 68, 108, 108, 10, 10, 1, 1, 7, 7, 7, 7, 68] 125 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 371 number of broken/clashed sets: 124 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220836 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=NC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 68, 68, 68, 68, 68, 87, 87, 86, 87, 87, 1, 2, 2, 2, 3, 3, 12, 12, 68, 68, 87, 87, 87, 87, 1] 125 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 124 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220836 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=NC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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: [87, 87, 87, 87, 125, 125, 125, 87, 87, 87, 21, 21, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 125, 125, 21, 21, 7, 7, 1, 1, 1, 1, 87] 125 rigid atoms, others: [34, 35, 36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 355 number of broken/clashed sets: 124 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220836 /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `1' /scratch/stefan/7769890/working/building/REAL300000220836/1 /scratch/stefan/7769890/working/building/REAL300000220836 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 1 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/850 `/scratch/stefan/7769890/working/3D/850' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=[NH+]C=C2)N1) `REAL300000220836.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220836/1/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: REAL300000220836 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=[NH+]C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 6, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [39, 39, 39, 39, 53, 53, 53, 39, 39, 39, 10, 10, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 5, 5, 39, 39, 39, 39, 53, 53, 10, 10, 1, 1, 5, 5, 5, 5, 39] 54 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 154 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: REAL300000220836 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=[NH+]C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 6, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 6, 6, 1, 1, 1, 1, 1, 10, 10, 39, 39, 39, 39, 39, 41, 41, 39, 39, 41, 41, 1, 2, 2, 2, 3, 3, 10, 10, 39, 39, 41, 41, 41, 41, 1] 54 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 39] set([4, 5, 6, 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: 94 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: REAL300000220836 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2=CC=[NH+]C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 6, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [41, 41, 41, 41, 54, 54, 54, 41, 41, 41, 12, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 54, 54, 12, 12, 5, 5, 1, 1, 1, 1, 41] 54 rigid atoms, others: [35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 142 number of broken/clashed sets: 53 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220836 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220836 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 1: /scratch/stefan/7769890/working/building/REAL300000220836/1.* 0: /scratch/stefan/7769890/working/building/REAL300000220836/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220836 Building REAL300000220837 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220837' /scratch/stefan/7769890/working/building/REAL300000220837 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220837 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220837/0 /scratch/stefan/7769890/working/building/REAL300000220837 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/851 `/scratch/stefan/7769890/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC=C2Cl)N1) `REAL300000220837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220837 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 30, 30, 30, 37, 37, 37, 30, 30, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 37, 37, 9, 9, 1, 1, 1, 30] 37 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 89 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: REAL300000220837 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC=C2Cl)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 30, 30, 20, 30, 30, 30, 1, 2, 2, 2, 3, 3, 10, 10, 30, 30, 30, 1] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 101 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220837 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220837 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220837/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220837 Building REAL300000220838 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220838' /scratch/stefan/7769890/working/building/REAL300000220838 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220838 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220838/0 /scratch/stefan/7769890/working/building/REAL300000220838 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/852 `/scratch/stefan/7769890/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(NS(C)(=O)=O)=C2)=N1) `REAL300000220838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220838 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(NS(C)(=O)=O)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 60, 89, 89, 32, 32, 32, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 1, 32, 32, 32, 32, 60, 60, 32, 5, 5, 1, 1, 1, 7, 13, 13, 13, 1] 201 rigid atoms, others: [33, 34, 35, 40, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 366 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220838 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(NS(C)(=O)=O)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 32, 32, 32, 32, 32, 134, 144, 144, 144, 32, 1, 2, 2, 2, 3, 3, 1, 9, 9, 32, 32, 32, 134, 144, 144, 144, 32] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 398 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220838 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220838 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220838/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220838 Building REAL300000220839 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220839' /scratch/stefan/7769890/working/building/REAL300000220839 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220839 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220839/0 /scratch/stefan/7769890/working/building/REAL300000220839 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/853 `/scratch/stefan/7769890/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(F)=C2F)=N1) `REAL300000220839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220839 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(F)=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [22, 22, 22, 22, 35, 35, 35, 22, 22, 22, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 35, 35, 22, 9, 9, 1, 1] 35 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 116 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220839 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(F)C(F)=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 1, 10, 10, 22, 22] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 62 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220839 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220839 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220839/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220839 Building REAL300000220840 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220840' /scratch/stefan/7769890/working/building/REAL300000220840 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220840 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220840/0 /scratch/stefan/7769890/working/building/REAL300000220840 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/854 `/scratch/stefan/7769890/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(C(F)(F)F)=C1) `REAL300000220840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220840 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [46, 30, 30, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 46, 46, 46, 30, 10, 10, 2, 2, 2, 3, 3, 1, 30, 30] 66 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 105 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: REAL300000220840 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 5, 5, 30, 30, 30, 30, 30, 49, 66, 66, 30, 30, 30, 1, 1, 1, 2, 2, 2, 1, 3, 3, 3, 1, 5, 5, 30, 30, 30, 49, 49, 30, 1, 1] 66 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 19, 20, 21, 25, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 236 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220840 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220840 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220840/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220840 Building REAL300000220841 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220841' /scratch/stefan/7769890/working/building/REAL300000220841 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220841 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220841/0 /scratch/stefan/7769890/working/building/REAL300000220841 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/855 `/scratch/stefan/7769890/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=C(Cl)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220841 none C=CCOC1=C(Cl)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', '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, 12, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 129, 58, 32, 32, 32, 32, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 32, 32, 32, 74, 142, 142, 142, 129, 129, 32, 9, 9, 2, 2, 2, 3, 3, 1, 32, 74, 74, 74] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 588 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220841 none C=CCOC1=C(Cl)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', '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, 12, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 10, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 32, 32, 32, 32, 32, 58, 95, 95, 32, 32, 32, 1, 1, 1, 3, 17, 17, 17, 10, 10, 1, 5, 5, 32, 32, 32, 58, 58, 32, 1, 4, 4, 4] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 41, 23, 24, 25] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 409 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220841 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220841 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220841/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220841 Building REAL300000220842 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220842' /scratch/stefan/7769890/working/building/REAL300000220842 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220842 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220842/0 /scratch/stefan/7769890/working/building/REAL300000220842 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/856 `/scratch/stefan/7769890/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC1CC1) `REAL300000220842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220842 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 28, 28, 28, 28, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 28, 28, 28, 85, 113, 113, 50, 50, 50, 28, 28, 9, 9, 2, 2, 2, 3, 3, 1, 28, 113, 113, 113, 113, 113] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 301 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220842 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 28, 28, 28, 28, 28, 51, 81, 81, 28, 28, 28, 1, 1, 1, 8, 15, 15, 3, 3, 3, 1, 1, 5, 5, 28, 28, 28, 51, 51, 28, 1, 15, 15, 15, 15, 15] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 20, 21, 22, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 329 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220842 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 15, 15, 15, 15, 15, 15, 42, 42, 113, 113, 113, 113, 113, 163, 201, 201, 113, 113, 113, 15, 7, 1, 1, 1, 1, 17, 17, 17, 15, 15, 42, 42, 113, 113, 113, 163, 163, 113, 15, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 650 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220842 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220842 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220842/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220842 Building REAL300000220843 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220843' /scratch/stefan/7769890/working/building/REAL300000220843 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220843 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220843/0 /scratch/stefan/7769890/working/building/REAL300000220843 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/857 `/scratch/stefan/7769890/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1N=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220843 none CCCN1N=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 117, 53, 53, 53, 53, 53, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 142, 142, 142, 142, 142, 117, 117, 53, 53, 12, 12, 3, 3, 2, 2, 2, 1] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 529 number of broken/clashed sets: 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: REAL300000220843 none CCCN1N=CC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 53, 53, 53, 53, 53, 85, 129, 129, 53, 53, 53, 11, 11, 11, 11, 11, 6, 6, 1, 1, 10, 10, 85, 85, 53, 53, 53, 53] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 475 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220843 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220843 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220843/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220843 Building REAL300000220844 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220844' /scratch/stefan/7769890/working/building/REAL300000220844 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220844 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220844/0 /scratch/stefan/7769890/working/building/REAL300000220844 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/858 `/scratch/stefan/7769890/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(F)(F)F)=NN2C)=N1) `REAL300000220844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220844 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(F)(F)F)=NN2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 37, 37, 37, 48, 48, 48, 37, 37, 37, 9, 9, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 37, 37, 37, 37, 48, 48, 37, 9, 9, 1, 2, 2, 2] 48 rigid atoms, others: [32, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 132 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220844 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(F)(F)F)=NN2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 2, 2, 2, 3, 3, 1, 12, 12, 37, 37, 37, 37] 48 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220844 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220844 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220844/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220844 Building REAL300000220845 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220845' /scratch/stefan/7769890/working/building/REAL300000220845 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220845 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220845/0 /scratch/stefan/7769890/working/building/REAL300000220845 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/859 `/scratch/stefan/7769890/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)OC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1) `REAL300000220845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220845 none COCC(C)OC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 156, 103, 58, 103, 18, 18, 33, 33, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 33, 33, 162, 162, 162, 156, 156, 103, 103, 103, 103, 33, 33, 10, 10, 2, 2, 2, 3, 3, 1, 33, 33] 201 rigid atoms, others: [44, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46]) total number of confs: 685 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220845 none COCC(C)OC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 23, 8, 4, 8, 1, 1, 1, 1, 1, 1, 5, 5, 33, 33, 33, 33, 33, 57, 88, 88, 33, 33, 33, 1, 1, 37, 37, 37, 23, 23, 8, 8, 8, 8, 1, 1, 5, 5, 33, 33, 33, 57, 57, 33, 1, 1] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 45, 46, 24, 25] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 418 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220845 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220845 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220845/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220845 Building REAL300000220846 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220846' /scratch/stefan/7769890/working/building/REAL300000220846 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220846 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220846/0 /scratch/stefan/7769890/working/building/REAL300000220846 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/860 `/scratch/stefan/7769890/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)S1) `REAL300000220846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220846 none CCCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 127, 63, 63, 63, 63, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 63, 166, 166, 166, 166, 166, 127, 127, 63, 63, 11, 11, 3, 3, 2, 2, 2, 1] 201 rigid atoms, others: [38, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 625 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220846 none CCCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'S.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, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 1, 1, 1, 1, 1, 1, 12, 12, 63, 63, 63, 63, 63, 90, 118, 118, 63, 63, 63, 1, 17, 17, 17, 17, 17, 8, 8, 1, 1, 12, 12, 90, 90, 63, 63, 63, 63] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 21, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220846 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220846 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220846/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220846 Building REAL300000220847 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220847' /scratch/stefan/7769890/working/building/REAL300000220847 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220847 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220847/0 /scratch/stefan/7769890/working/building/REAL300000220847 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/861 `/scratch/stefan/7769890/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CN=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220847 none CCOC1=CN=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 112, 47, 47, 46, 47, 47, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 47, 161, 161, 161, 161, 161, 47, 47, 12, 12, 3, 3, 2, 2, 2, 1, 47] 201 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 465 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: REAL300000220847 none CCOC1=CN=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 46, 46, 47, 47, 47, 76, 110, 110, 47, 47, 47, 1, 20, 20, 20, 20, 20, 1, 1, 7, 7, 76, 76, 47, 47, 47, 47, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 22, 38, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 436 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220847 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220847 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220847/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220847 Building REAL300000220848 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220848' /scratch/stefan/7769890/working/building/REAL300000220848 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220848 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220848/0 /scratch/stefan/7769890/working/building/REAL300000220848 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/862 `/scratch/stefan/7769890/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CS3)C=C2)N1) `REAL300000220848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220848 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CS3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [19, 19, 19, 19, 29, 31, 31, 19, 19, 19, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 19, 19, 19, 19, 29, 29, 3, 3, 1, 1, 11, 11, 11, 1, 1, 19] 51 rigid atoms, others: [32, 33, 37, 38, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39]) total number of confs: 104 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220848 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CS3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 19, 19, 11, 17, 39, 39, 39, 39, 19, 19, 1, 2, 2, 2, 3, 3, 11, 11, 19, 19, 39, 39, 39, 19, 19, 1] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 132 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220848 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CS3)C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [39, 39, 39, 39, 51, 51, 51, 39, 39, 39, 17, 17, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 39, 51, 51, 17, 17, 11, 11, 1, 1, 1, 11, 11, 39] 51 rigid atoms, others: [34, 35, 36, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 164 number of broken/clashed sets: 51 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220848 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220848 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220848/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220848 Building REAL300000220849 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220849' /scratch/stefan/7769890/working/building/REAL300000220849 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220849 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220849/0 /scratch/stefan/7769890/working/building/REAL300000220849 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/863 `/scratch/stefan/7769890/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2CCC2=CC=CC=C2)=N1) `REAL300000220849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220849 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2CCC2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 97, 121, 121, 56, 56, 56, 10, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 56, 56, 56, 56, 97, 97, 56, 10, 10, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 436 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220849 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2CCC2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 56, 56, 56, 56, 56, 132, 132, 132, 132, 132, 132, 132, 1, 2, 2, 2, 3, 3, 1, 11, 11, 56, 56, 132, 132, 132, 132, 132, 132, 132, 132, 132] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 442 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220849 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2CCC2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 132, 132, 201, 201, 201, 132, 132, 132, 35, 35, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 201, 201, 132, 35, 35, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 610 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220849 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220849 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220849/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220849 Building REAL300000220850 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220850' /scratch/stefan/7769890/working/building/REAL300000220850 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220850 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220850/0 /scratch/stefan/7769890/working/building/REAL300000220850 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/864 `/scratch/stefan/7769890/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C(C)C)=C2)N1) `REAL300000220850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220850 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C(C)C)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 33, 33, 33, 56, 61, 61, 33, 33, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 33, 33, 33, 33, 56, 56, 5, 5, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 1, 33] 89 rigid atoms, others: [32, 40, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 225 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220850 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C(C)C)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 33, 33, 19, 33, 33, 58, 58, 33, 1, 2, 2, 2, 3, 3, 10, 10, 33, 33, 31, 58, 58, 58, 58, 58, 58, 58, 33, 1] 89 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 41] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 275 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220850 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220850 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220850/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220850 Building REAL300000220851 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220851' /scratch/stefan/7769890/working/building/REAL300000220851 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220851 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220851/0 /scratch/stefan/7769890/working/building/REAL300000220851 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/865 `/scratch/stefan/7769890/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2Cl)=N1) `REAL300000220851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220851 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [41, 41, 41, 41, 44, 44, 44, 41, 41, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 44, 44, 41, 11, 11, 1, 2, 2, 2] 44 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 87 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: REAL300000220851 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 3, 3, 1, 12, 12, 41, 41, 41, 41] 44 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 89 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220851 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220851 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220851/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220851 Building REAL300000220852 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220852' /scratch/stefan/7769890/working/building/REAL300000220852 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220852 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220852/0 /scratch/stefan/7769890/working/building/REAL300000220852 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/866 `/scratch/stefan/7769890/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(F)=C2OCC(F)(F)F)=N1) `REAL300000220852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220852 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(F)=C2OCC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 64, 119, 146, 146, 64, 64, 64, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 64, 64, 64, 64, 119, 119, 64, 9, 9, 1, 1, 1, 8, 8] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 546 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220852 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(F)=C2OCC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 64, 64, 64, 64, 64, 64, 64, 84, 144, 144, 144, 144, 1, 2, 2, 2, 3, 3, 1, 12, 12, 64, 64, 64, 144, 144] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 470 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220852 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220852 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220852/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220852 Building REAL300000220853 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220853' /scratch/stefan/7769890/working/building/REAL300000220853 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220853 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220853/0 /scratch/stefan/7769890/working/building/REAL300000220853 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/867 `/scratch/stefan/7769890/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(Br)N2C)=N1) `REAL300000220853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220853 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(Br)N2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Br', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 17, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 30, 30, 30, 43, 43, 43, 30, 30, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 43, 43, 30, 10, 10, 1, 2, 2, 2] 43 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 132 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: REAL300000220853 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(Br)N2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Br', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 17, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 30, 30, 30, 30, 30, 30, 1, 2, 2, 2, 3, 3, 1, 11, 11, 30, 30, 30, 30] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 74 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220853 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220853 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220853/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220853 Building REAL300000220854 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220854' /scratch/stefan/7769890/working/building/REAL300000220854 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220854 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220854/0 /scratch/stefan/7769890/working/building/REAL300000220854 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/868 `/scratch/stefan/7769890/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C(C)(C)C) `REAL300000220854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220854 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 17, 9, 24, 24, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 2, 2, 2, 3, 3, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 33 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220854 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 24, 24, 24, 24, 24, 33, 33, 33, 24, 24, 24, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 5, 5, 24, 24, 24, 33, 33, 24, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 20, 21, 22, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220854 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220854 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220854/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220854 Building REAL300000220855 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220855' /scratch/stefan/7769890/working/building/REAL300000220855 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220855 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220855/0 /scratch/stefan/7769890/working/building/REAL300000220855 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/869 `/scratch/stefan/7769890/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(CC3CCC3)=C2)N1) `REAL300000220855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220855 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(CC3CCC3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 58, 72, 72, 35, 35, 35, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 1, 35, 35, 35, 35, 58, 58, 6, 6, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 16, 16, 1, 35] 201 rigid atoms, others: [32, 33, 34, 44, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45]) total number of confs: 285 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220855 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(CC3CCC3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 35, 35, 22, 35, 35, 86, 137, 137, 137, 35, 1, 2, 2, 2, 3, 3, 12, 12, 35, 35, 31, 86, 86, 137, 137, 137, 137, 137, 137, 137, 35, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 45, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 572 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220855 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(CC3CCC3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 137, 201, 201, 201, 137, 137, 137, 54, 54, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 16, 137, 137, 137, 137, 201, 201, 54, 54, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 16, 137] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45]) total number of confs: 636 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220855 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220855 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220855/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220855 Building REAL300000220856 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220856' /scratch/stefan/7769890/working/building/REAL300000220856 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220856 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220856/0 /scratch/stefan/7769890/working/building/REAL300000220856 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/870 `/scratch/stefan/7769890/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C(=O)[O-]) `REAL300000220856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220856 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [63, 38, 38, 38, 38, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 38, 38, 38, 61, 61, 63, 63, 63, 38, 38, 13, 12, 3, 3, 2, 2, 2, 1, 38] 126 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 231 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: REAL300000220856 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 7, 7, 38, 38, 38, 38, 38, 60, 85, 85, 38, 38, 38, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 7, 7, 60, 60, 38, 38, 38, 38, 1] 126 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 38, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 293 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220856 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220856 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220856/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220856 Building REAL300000220857 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220857' /scratch/stefan/7769890/working/building/REAL300000220857 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220857 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220857/0 /scratch/stefan/7769890/working/building/REAL300000220857 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/871 `/scratch/stefan/7769890/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(Cl)C=C1O) `REAL300000220857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220857 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(Cl)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [61, 39, 39, 39, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 39, 39, 39, 39, 39, 61, 61, 61, 39, 11, 11, 2, 2, 2, 3, 3, 1, 39, 78] 158 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 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: 158 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220857 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(Cl)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 1, 1, 1, 1, 9, 9, 39, 39, 39, 39, 39, 61, 79, 79, 39, 39, 39, 1, 1, 1, 1, 1, 4, 4, 4, 1, 9, 9, 39, 39, 39, 61, 61, 39, 1, 2] 158 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 36, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 272 number of broken/clashed sets: 158 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220857 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220857 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220857/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220857 Building REAL300000220858 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220858' /scratch/stefan/7769890/working/building/REAL300000220858 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220858 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220858/0 /scratch/stefan/7769890/working/building/REAL300000220858 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/872 `/scratch/stefan/7769890/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C(=O)[O-])=CC=C2F)N1) `REAL300000220858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220858 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C(=O)[O-])=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 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: [39, 39, 39, 39, 47, 47, 47, 39, 39, 39, 11, 11, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 39, 39, 39, 39, 47, 47, 11, 11, 1, 1, 1, 35] 47 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 115 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220858 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C(=O)[O-])=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 8, 8, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 3, 3, 8, 8, 39, 39, 39, 1] 47 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 83 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220858 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220858 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220858/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220858 Building REAL300000220859 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220859' /scratch/stefan/7769890/working/building/REAL300000220859 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220859 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220859/0 /scratch/stefan/7769890/working/building/REAL300000220859 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/873 `/scratch/stefan/7769890/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=C(Cl)N=CC=C3S2)N1) `REAL300000220859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220859 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=C(Cl)N=CC=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [34, 34, 34, 34, 46, 46, 46, 33, 34, 33, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 46, 46, 12, 12, 1, 1, 1, 34] 46 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 131 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220859 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=C(Cl)N=CC=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 34, 34, 34, 34, 34, 33, 34, 34, 34, 1, 2, 2, 2, 3, 3, 11, 11, 34, 33, 34, 1] 46 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 83 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220859 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220859 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220859/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220859 Building REAL300000220860 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220860' /scratch/stefan/7769890/working/building/REAL300000220860 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220860 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220860/0 /scratch/stefan/7769890/working/building/REAL300000220860 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/874 `/scratch/stefan/7769890/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=NC(Cl)=C3S2)N1) `REAL300000220860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220860 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=NC(Cl)=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [31, 31, 31, 31, 38, 38, 38, 30, 31, 30, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 38, 38, 13, 13, 1, 1, 1, 31] 38 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 98 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: REAL300000220860 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=CC=NC(Cl)=C3S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 31, 31, 31, 31, 30, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 11, 11, 31, 31, 31, 1] 38 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 75 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220860 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220860 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220860/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220860 Building REAL300000220861 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220861' /scratch/stefan/7769890/working/building/REAL300000220861 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220861 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220861/0 /scratch/stefan/7769890/working/building/REAL300000220861 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/875 `/scratch/stefan/7769890/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(OC(F)(F)F)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220861 none COC1=CC=CC(OC(F)(F)F)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [64, 42, 42, 42, 14, 42, 42, 42, 63, 83, 83, 83, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 64, 64, 64, 42, 15, 42, 11, 11, 2, 2, 2, 3, 3, 1] 105 rigid atoms, others: [40, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 351 number of broken/clashed sets: 104 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220861 none COC1=CC=CC(OC(F)(F)F)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 1, 1, 7, 7, 42, 42, 42, 42, 42, 62, 89, 89, 42, 42, 42, 4, 4, 4, 1, 1, 1, 7, 7, 42, 42, 42, 62, 62, 40] 105 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 12, 13, 30, 31] set([0, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 336 number of broken/clashed sets: 104 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220861 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220861 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220861/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220861 Building REAL300000220862 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220862' /scratch/stefan/7769890/working/building/REAL300000220862 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220862 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220862/0 /scratch/stefan/7769890/working/building/REAL300000220862 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/876 `/scratch/stefan/7769890/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(Br)C=C1F) `REAL300000220862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220862 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(Br)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 29, 29, 11, 27, 29, 29, 29, 29, 11, 11, 2, 2, 2, 3, 3, 1, 29] 37 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 134 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: REAL300000220862 none CC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(Br)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 7, 7, 29, 29, 29, 29, 29, 37, 37, 37, 29, 29, 29, 1, 1, 1, 1, 1, 2, 2, 2, 1, 7, 7, 29, 29, 29, 37, 37, 29, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 35, 18, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 97 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220862 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220862 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220862/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220862 Building REAL300000220863 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220863' /scratch/stefan/7769890/working/building/REAL300000220863 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220863 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220863/0 /scratch/stefan/7769890/working/building/REAL300000220863 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/877 `/scratch/stefan/7769890/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220863 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 65, 65, 65, 65, 65, 105, 65, 65, 98, 98, 65, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 92, 92, 92, 65, 105, 105, 105, 65, 12, 12, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [42, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 376 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220863 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 3, 3, 1, 1, 1, 9, 9, 65, 65, 65, 65, 65, 101, 143, 143, 65, 65, 65, 4, 4, 4, 1, 3, 3, 3, 1, 9, 9, 65, 65, 65, 101, 101, 65] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 11, 12, 34, 13, 30] set([0, 6, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 485 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220863 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220863 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220863/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220863 Building REAL300000220864 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220864' /scratch/stefan/7769890/working/building/REAL300000220864 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220864 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220864/0 /scratch/stefan/7769890/working/building/REAL300000220864 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/878 `/scratch/stefan/7769890/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C(C(=O)[O-])=C2)N1) `REAL300000220864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220864 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C(C(=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 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: [31, 31, 31, 31, 51, 63, 63, 31, 31, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 31, 31, 31, 31, 51, 51, 6, 6, 1, 1, 1, 31] 63 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 217 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: REAL300000220864 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C(C(=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 31, 31, 31, 31, 31, 31, 47, 47, 31, 1, 2, 2, 2, 3, 3, 12, 12, 31, 31, 31, 1] 63 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 145 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220864 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220864 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220864/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220864 Building REAL300000220865 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220865' /scratch/stefan/7769890/working/building/REAL300000220865 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220865 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220865/0 /scratch/stefan/7769890/working/building/REAL300000220865 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/879 `/scratch/stefan/7769890/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(CC(=O)[O-])C=C2)N1) `REAL300000220865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220865 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(CC(=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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, 15, 15, 15, 25, 31, 31, 15, 15, 15, 4, 4, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 15, 15, 15, 15, 25, 25, 4, 4, 1, 1, 2, 2, 1, 1, 15] 31 rigid atoms, others: [32, 35, 36, 12, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37]) total number of confs: 123 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: REAL300000220865 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(CC(=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 15, 15, 9, 9, 19, 19, 19, 15, 15, 1, 2, 2, 2, 3, 3, 9, 9, 15, 15, 19, 19, 15, 15, 1] 31 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 120 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220865 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220865 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220865/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220865 Building REAL300000220866 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220866' /scratch/stefan/7769890/working/building/REAL300000220866 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220866 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220866/0 /scratch/stefan/7769890/working/building/REAL300000220866 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/880 `/scratch/stefan/7769890/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=N1) `REAL300000220866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220866 none CCOC(=O)C1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.ar', '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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 139, 130, 69, 130, 69, 68, 69, 69, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 69, 158, 158, 158, 158, 158, 68, 69, 69, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [40, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 422 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220866 none CCOC(=O)C1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.ar', '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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 12, 68, 68, 69, 69, 69, 106, 135, 135, 69, 69, 69, 1, 28, 28, 28, 27, 27, 1, 1, 1, 12, 12, 69, 69, 69, 106, 106, 69] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 24, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 527 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220866 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220866 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220866/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220866 Building REAL300000220867 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220867' /scratch/stefan/7769890/working/building/REAL300000220867 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220867 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220867/0 /scratch/stefan/7769890/working/building/REAL300000220867 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/881 `/scratch/stefan/7769890/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CC(C(=O)[O-])=C2)=N1) `REAL300000220867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220867 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CC(C(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [23, 23, 23, 23, 33, 33, 33, 23, 23, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 23, 23, 23, 33, 33, 23, 6, 6, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 99 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220867 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(Br)=CC(C(=O)[O-])=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 3, 1, 10, 10, 23, 23, 23] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 63 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220867 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220867 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220867/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220867 Building REAL300000220868 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220868' /scratch/stefan/7769890/working/building/REAL300000220868 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220868 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220868/0 /scratch/stefan/7769890/working/building/REAL300000220868 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/882 `/scratch/stefan/7769890/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CN(C)N=C3)=N2)=N1) `REAL300000220868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220868 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CN(C)N=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 8, 5, 8, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 55, 55, 55, 72, 76, 76, 55, 55, 55, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 55, 56, 56, 56, 72, 72, 52, 12, 11, 1, 5, 5, 5, 5, 5] 108 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 209 number of broken/clashed sets: 107 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220868 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CN(C)N=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 8, 5, 8, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 55, 55, 55, 55, 89, 89, 89, 89, 89, 55, 1, 2, 2, 2, 3, 3, 1, 12, 12, 55, 89, 89, 89, 89, 89] 108 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 168 number of broken/clashed sets: 107 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220868 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C3=CN(C)N=C3)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 8, 5, 8, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [89, 89, 89, 89, 108, 108, 108, 89, 89, 89, 31, 31, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 89, 89, 89, 89, 108, 108, 87, 31, 31, 5, 1, 2, 2, 2, 1] 108 rigid atoms, others: [34, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 266 number of broken/clashed sets: 107 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220868 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220868 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220868/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220868 Building REAL300000220869 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220869' /scratch/stefan/7769890/working/building/REAL300000220869 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220869 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220869/0 /scratch/stefan/7769890/working/building/REAL300000220869 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/883 `/scratch/stefan/7769890/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1Cl) `REAL300000220869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220869 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [47, 30, 30, 30, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 30, 30, 30, 30, 47, 47, 47, 30, 11, 11, 2, 2, 2, 3, 3, 1, 30, 30] 59 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 109 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: REAL300000220869 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 30, 30, 30, 30, 30, 46, 59, 59, 30, 30, 30, 1, 1, 1, 1, 4, 4, 4, 1, 6, 6, 30, 30, 30, 46, 46, 30, 1, 1] 59 rigid atoms, others: [1, 2, 3, 4, 5, 35, 19, 20, 21, 22, 36, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 200 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220869 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220869 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220869/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220869 Building REAL300000220870 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220870' /scratch/stefan/7769890/working/building/REAL300000220870 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220870 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220870/0 /scratch/stefan/7769890/working/building/REAL300000220870 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/884 `/scratch/stefan/7769890/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2CC2CCC2)=N1) `REAL300000220870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220870 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2CC2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 78, 107, 107, 47, 47, 47, 10, 10, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 47, 47, 47, 47, 78, 78, 47, 10, 10, 1, 1, 6, 6, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 412 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220870 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2CC2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 47, 47, 47, 47, 47, 106, 130, 130, 130, 1, 2, 2, 2, 3, 3, 1, 11, 11, 47, 47, 106, 106, 130, 130, 130, 130, 130, 130, 130] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 462 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220870 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=NN2CC2CCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 201, 201, 201, 130, 130, 130, 50, 50, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 130, 130, 130, 130, 201, 201, 130, 50, 50, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 660 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220870 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220870 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220870/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220870 Building REAL300000220871 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220871' /scratch/stefan/7769890/working/building/REAL300000220871 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220871 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220871/0 /scratch/stefan/7769890/working/building/REAL300000220871 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/885 `/scratch/stefan/7769890/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(F)C=C3)N=N2)=N1) `REAL300000220871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220871 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(F)C=C3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 61, 63, 63, 53, 53, 53, 12, 12, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 1, 53, 53, 53, 53, 61, 61, 53, 12, 12, 1, 4, 4, 4, 4] 63 rigid atoms, others: [34, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 140 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220871 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(F)C=C3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 53, 53, 53, 57, 57, 53, 55, 57, 57, 53, 53, 1, 2, 2, 2, 3, 3, 1, 11, 11, 53, 57, 57, 57, 57] 63 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 123 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220871 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3=CC=C(F)C=C3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 57, 57, 57, 63, 63, 63, 57, 57, 57, 25, 25, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 57, 57, 57, 57, 63, 63, 57, 25, 25, 4, 1, 1, 1, 1] 63 rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 135 number of broken/clashed sets: 62 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220871 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220871 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220871/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220871 Building REAL300000220872 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220872' /scratch/stefan/7769890/working/building/REAL300000220872 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220872 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220872/0 /scratch/stefan/7769890/working/building/REAL300000220872 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/886 `/scratch/stefan/7769890/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2CC(F)(F)F)=N1) `REAL300000220872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220872 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2CC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 96, 144, 144, 58, 58, 58, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 58, 58, 58, 58, 96, 96, 58, 9, 9, 1, 1, 1, 1, 6, 6] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 514 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220872 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2CC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 58, 58, 25, 58, 58, 58, 139, 139, 139, 139, 1, 2, 2, 2, 3, 3, 1, 12, 12, 58, 58, 51, 58, 139, 139] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 585 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220872 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220872 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220872/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220872 Building REAL300000220873 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220873' /scratch/stefan/7769890/working/building/REAL300000220873 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220873 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220873/0 /scratch/stefan/7769890/working/building/REAL300000220873 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/887 `/scratch/stefan/7769890/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2Br)=N1) `REAL300000220873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220873 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 41, 41, 41, 35, 35, 35, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 41, 41, 35, 9, 9, 1, 2, 2, 2] 41 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 95 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220873 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 1, 9, 9, 35, 35, 35, 35] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 76 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220873 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220873 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220873/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220873 Building REAL300000220874 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220874' /scratch/stefan/7769890/working/building/REAL300000220874 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220874 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220874/0 /scratch/stefan/7769890/working/building/REAL300000220874 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/888 `/scratch/stefan/7769890/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)C=C2[N+](=O)[O-])=N1) `REAL300000220874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220874 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)C=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [21, 21, 21, 21, 29, 29, 29, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 21, 21, 21, 21, 29, 29, 21, 5, 5, 1, 1, 1] 29 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 89 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: REAL300000220874 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)C=C2[N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 21, 21, 18, 19, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 11, 11, 21, 21, 21] 29 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220874 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220874 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220874/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220874 Building REAL300000220875 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220875' /scratch/stefan/7769890/working/building/REAL300000220875 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220875 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220875/0 /scratch/stefan/7769890/working/building/REAL300000220875 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/889 `/scratch/stefan/7769890/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(F)=C1) `REAL300000220875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220875 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [28, 18, 28, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 3, 3, 2, 2, 2, 1, 28] 38 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) 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: REAL300000220875 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 1, 10, 10, 28, 28, 28, 28, 28, 38, 38, 38, 28, 28, 28, 1, 1, 1, 2, 2, 2, 1, 1, 10, 10, 38, 38, 28, 28, 28, 26, 1] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220875 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220875 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220875/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220875 Building REAL300000220876 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220876' /scratch/stefan/7769890/working/building/REAL300000220876 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220876 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220876/0 /scratch/stefan/7769890/working/building/REAL300000220876 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/890 `/scratch/stefan/7769890/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220876 none CC(=O)NC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [81, 81, 81, 29, 29, 29, 29, 29, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 81, 81, 81, 81, 29, 29, 29, 12, 12, 3, 3, 2, 2, 2, 1, 29] 132 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 224 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: REAL300000220876 none CC(=O)NC1=CC=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 49, 59, 59, 29, 29, 29, 1, 5, 5, 5, 5, 1, 1, 1, 7, 7, 49, 49, 29, 29, 29, 29, 1] 132 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 39, 23, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 212 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220876 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220876 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220876/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220876 Building REAL300000220877 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220877' /scratch/stefan/7769890/working/building/REAL300000220877 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220877 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220877/0 /scratch/stefan/7769890/working/building/REAL300000220877 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/891 `/scratch/stefan/7769890/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC) `REAL300000220877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220877 none COC1=CC(Cl)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.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, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [119, 67, 67, 67, 67, 67, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 67, 67, 67, 124, 119, 119, 119, 67, 12, 12, 2, 2, 2, 3, 3, 1, 67, 124, 124, 124] 159 rigid atoms, others: [36, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40]) total number of confs: 293 number of broken/clashed sets: 159 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220877 none COC1=CC(Cl)=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.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, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 67, 67, 67, 67, 67, 95, 129, 129, 67, 67, 67, 1, 1, 1, 4, 3, 3, 3, 1, 9, 9, 67, 67, 67, 95, 95, 67, 1, 4, 4, 4] 159 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 28, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 397 number of broken/clashed sets: 159 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220877 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220877 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220877/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220877 Building REAL300000220878 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220878' /scratch/stefan/7769890/working/building/REAL300000220878 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220878 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220878/0 /scratch/stefan/7769890/working/building/REAL300000220878 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/892 `/scratch/stefan/7769890/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3CCOC3)N=N2)=N1) `REAL300000220878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220878 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3CCOC3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 35, 35, 55, 60, 60, 36, 36, 36, 7, 7, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 1, 1, 36, 36, 36, 36, 55, 55, 36, 7, 7, 1, 8, 8, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [33, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 258 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220878 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3CCOC3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 36, 36, 36, 104, 146, 146, 146, 146, 36, 35, 1, 2, 2, 2, 3, 3, 1, 12, 12, 36, 104, 104, 146, 146, 146, 146, 146, 146, 146] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 511 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220878 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3CCOC3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 201, 201, 201, 146, 146, 146, 58, 58, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 23, 23, 146, 146, 146, 146, 201, 201, 146, 58, 58, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 587 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220878 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220878 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220878/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220878 Building REAL300000220879 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220879' /scratch/stefan/7769890/working/building/REAL300000220879 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220879 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220879/0 /scratch/stefan/7769890/working/building/REAL300000220879 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/893 `/scratch/stefan/7769890/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(CC(F)(F)F)C=C2)=N1) `REAL300000220879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220879 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(CC(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 23, 29, 29, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 13, 13, 13, 13, 23, 23, 13, 4, 4, 1, 1, 4, 4, 1, 1] 57 rigid atoms, others: [33, 34, 37, 38, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 117 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220879 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(CC(F)(F)F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 13, 13, 9, 9, 35, 35, 35, 35, 13, 13, 1, 2, 2, 2, 3, 3, 1, 9, 9, 13, 13, 35, 35, 13, 13] 57 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220879 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220879 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220879/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220879 Building REAL300000220880 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220880' /scratch/stefan/7769890/working/building/REAL300000220880 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220880 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220880/0 /scratch/stefan/7769890/working/building/REAL300000220880 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/894 `/scratch/stefan/7769890/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3CCCCC3=NN2C)N1) `REAL300000220880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220880 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3CCCCC3=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 35, 35, 35, 45, 45, 45, 35, 35, 35, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 45, 45, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 35] 45 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42]) total number of confs: 115 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: REAL300000220880 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3CCCCC3=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1] 45 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 42] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 77 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220880 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220880 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220880/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220880 Building REAL300000220881 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220881' /scratch/stefan/7769890/working/building/REAL300000220881 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220881 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220881/0 /scratch/stefan/7769890/working/building/REAL300000220881 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/895 `/scratch/stefan/7769890/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CS1) `REAL300000220881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220881 none CC1=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'S.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, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [29, 29, 29, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 3, 3, 2, 2, 2, 1, 29] 40 rigid atoms, others: [34, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) 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: REAL300000220881 none CC1=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'S.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, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 29, 29, 40, 40, 40, 29, 29, 29, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 40, 40, 29, 29, 29, 29, 1] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220881 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220881 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220881/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220881 Building REAL300000220882 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220882' /scratch/stefan/7769890/working/building/REAL300000220882 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220882 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220882/0 /scratch/stefan/7769890/working/building/REAL300000220882 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/896 `/scratch/stefan/7769890/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(C)N1) `REAL300000220882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220882 none CCOC(=O)C1=C(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 113, 112, 53, 112, 53, 53, 53, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 53, 53, 53, 142, 142, 142, 142, 142, 53, 53, 53, 11, 11, 2, 2, 2, 3, 3, 1, 53, 53, 53, 53] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 456 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220882 none CCOC(=O)C1=C(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 53, 53, 53, 53, 53, 94, 123, 123, 53, 53, 53, 1, 1, 1, 11, 11, 11, 10, 10, 2, 2, 2, 7, 7, 53, 53, 53, 94, 94, 53, 2, 2, 2, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 45, 23, 24, 25] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 473 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220882 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220882 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220882/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220882 Building REAL300000220883 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220883' /scratch/stefan/7769890/working/building/REAL300000220883 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220883 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220883/0 /scratch/stefan/7769890/working/building/REAL300000220883 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/897 `/scratch/stefan/7769890/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N1) `REAL300000220883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220883 none CCOC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.pl3', '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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 112, 111, 61, 111, 61, 61, 61, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 61, 151, 151, 151, 151, 151, 61, 61, 10, 10, 3, 3, 2, 2, 2, 1, 61] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 486 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: REAL300000220883 none CCOC(=O)C1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'N.pl3', '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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 6, 1, 6, 1, 1, 1, 1, 1, 13, 13, 60, 60, 61, 61, 61, 92, 121, 121, 61, 61, 61, 1, 17, 17, 17, 16, 16, 1, 1, 13, 13, 92, 92, 61, 61, 61, 61, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 39, 23, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 446 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220883 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220883 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220883/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220883 Building REAL300000220884 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220884' /scratch/stefan/7769890/working/building/REAL300000220884 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220884 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220884/0 /scratch/stefan/7769890/working/building/REAL300000220884 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/898 `/scratch/stefan/7769890/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(Cl)C(F)=C2)=N1) `REAL300000220884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220884 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(Cl)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 16, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 25, 25, 25, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 25, 25, 19, 5, 5, 1, 1] 25 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 65 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: REAL300000220884 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN=C(Cl)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 16, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 1, 7, 7, 19, 19] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220884 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220884 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220884/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220884 Building REAL300000220885 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220885' /scratch/stefan/7769890/working/building/REAL300000220885 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220885 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220885/0 /scratch/stefan/7769890/working/building/REAL300000220885 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/899 `/scratch/stefan/7769890/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)N1) `REAL300000220885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220885 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 24, 24, 24, 34, 34, 34, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 24, 24, 24, 24, 34, 34, 5, 5, 1, 1, 4, 4, 2, 4, 4, 1, 24] 34 rigid atoms, others: [34, 35, 41, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 42]) total number of confs: 105 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: REAL300000220885 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 24, 24, 22, 23, 26, 26, 24, 26, 26, 24, 24, 24, 1, 2, 2, 2, 3, 3, 9, 9, 24, 24, 26, 26, 24, 26, 26, 24, 1] 34 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 26, 42] set([4, 5, 6, 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, 41]) total number of confs: 89 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220885 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [26, 26, 26, 26, 34, 34, 34, 25, 26, 26, 11, 11, 3, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 26, 26, 26, 26, 34, 34, 11, 11, 4, 4, 1, 1, 1, 1, 1, 4, 26] 34 rigid atoms, others: [36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 106 number of broken/clashed sets: 34 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220885 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220885 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220885/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220885 Building REAL300000220886 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220886' /scratch/stefan/7769890/working/building/REAL300000220886 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220886 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220886/0 /scratch/stefan/7769890/working/building/REAL300000220886 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/900 `/scratch/stefan/7769890/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C(F)=C2F)=N1) `REAL300000220886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220886 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C(F)=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 15, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [22, 22, 22, 22, 35, 35, 35, 22, 22, 22, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 35, 35, 22, 9, 9, 1, 1] 35 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 116 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220886 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)C(F)=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 15, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 1, 10, 10, 22, 22] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 62 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220886 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220886 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220886/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220886 Building REAL300000220887 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220887' /scratch/stefan/7769890/working/building/REAL300000220887 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220887 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220887/0 /scratch/stefan/7769890/working/building/REAL300000220887 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/901 `/scratch/stefan/7769890/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=C(Br)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220887 none COC1=NC=C(Br)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 17, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [69, 67, 67, 67, 67, 67, 67, 67, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 69, 69, 69, 67, 67, 12, 12, 2, 2, 2, 3, 3, 1] 91 rigid atoms, others: [35, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 119 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: REAL300000220887 none COC1=NC=C(Br)C=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 17, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 67, 67, 67, 67, 67, 91, 91, 91, 67, 67, 67, 4, 4, 4, 1, 1, 11, 11, 67, 67, 67, 91, 91, 67] 91 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27] set([0, 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: 242 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220887 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220887 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220887/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220887 Building REAL300000220888 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220888' /scratch/stefan/7769890/working/building/REAL300000220888 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220888 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220888/0 /scratch/stefan/7769890/working/building/REAL300000220888 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/902 `/scratch/stefan/7769890/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(=O)OC(C)(C)C)=NN2C)=N1) `REAL300000220888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220888 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(=O)OC(C)(C)C)=NN2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 92, 108, 108, 61, 61, 61, 10, 10, 1, 1, 1, 1, 1, 7, 7, 16, 18, 18, 18, 1, 1, 1, 61, 61, 61, 61, 92, 92, 61, 10, 10, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2] 201 rigid atoms, others: [35, 12, 13, 14, 15, 16, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 376 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220888 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(=O)OC(C)(C)C)=NN2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 61, 61, 61, 120, 120, 166, 167, 167, 167, 61, 61, 61, 1, 2, 2, 2, 3, 3, 1, 11, 11, 61, 167, 167, 167, 167, 167, 167, 167, 167, 167, 61, 61, 61] 201 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 379 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220888 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220888 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220888/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220888 Building REAL300000220889 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220889' /scratch/stefan/7769890/working/building/REAL300000220889 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220889 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220889/0 /scratch/stefan/7769890/working/building/REAL300000220889 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/903 `/scratch/stefan/7769890/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Br)SC=C2)=N1) `REAL300000220889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220889 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Br)SC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 17, 14, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [33, 33, 33, 33, 43, 43, 43, 33, 33, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 43, 43, 33, 9, 9, 1, 1] 43 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 111 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: REAL300000220889 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Br)SC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 17, 14, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 33, 33, 33, 33, 33, 1, 2, 2, 2, 3, 3, 1, 9, 9, 33, 33] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 74 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220889 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220889 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220889/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220889 Building REAL300000220890 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220890' /scratch/stefan/7769890/working/building/REAL300000220890 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220890 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220890/0 /scratch/stefan/7769890/working/building/REAL300000220890 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/904 `/scratch/stefan/7769890/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(F)C=C1OC) `REAL300000220890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220890 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(F)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 15, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 149, 46, 46, 46, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 46, 46, 46, 46, 46, 80, 168, 168, 168, 168, 168, 46, 11, 11, 2, 2, 2, 3, 3, 1, 46, 80, 80, 80] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 411 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220890 none CCOC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(F)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 15, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 9, 1, 1, 1, 1, 1, 9, 9, 46, 46, 46, 46, 46, 79, 117, 117, 46, 46, 46, 1, 1, 1, 1, 1, 3, 22, 22, 22, 22, 22, 1, 9, 9, 46, 46, 46, 79, 79, 46, 1, 4, 4, 4] 201 rigid atoms, others: [2, 3, 4, 5, 6, 40, 20, 21, 22, 23, 24, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 486 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220890 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220890 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220890/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220890 Building REAL300000220891 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220891' /scratch/stefan/7769890/working/building/REAL300000220891 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220891 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220891/0 /scratch/stefan/7769890/working/building/REAL300000220891 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/905 `/scratch/stefan/7769890/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C3=CC=CC=C23)N1) `REAL300000220891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220891 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [31, 31, 31, 31, 41, 41, 41, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 41, 41, 9, 9, 1, 1, 1, 1, 1, 1, 31] 41 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 107 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: REAL300000220891 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(F)C3=CC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 10, 10, 31, 31, 31, 31, 31, 31, 1] 41 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 75 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220891 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220891 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220891/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220891 Building REAL300000220892 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220892' /scratch/stefan/7769890/working/building/REAL300000220892 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220892 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220892/0 /scratch/stefan/7769890/working/building/REAL300000220892 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/906 `/scratch/stefan/7769890/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CN=C2Br)=N1) `REAL300000220892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220892 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CN=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 29, 29, 29, 16, 16, 16, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 29, 29, 16, 7, 7, 1, 1, 1] 29 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 107 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: REAL300000220892 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CN=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 3, 3, 1, 9, 9, 16, 16, 16] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220892 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220892 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220892/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220892 Building REAL300000220893 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220893' /scratch/stefan/7769890/working/building/REAL300000220893 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220893 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220893/0 /scratch/stefan/7769890/working/building/REAL300000220893 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/907 `/scratch/stefan/7769890/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)F)N=C2)=N1) `REAL300000220893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220893 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)F)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 59, 59, 59, 35, 35, 35, 5, 5, 1, 1, 1, 1, 1, 1, 12, 12, 1, 1, 35, 35, 35, 35, 59, 59, 35, 5, 5, 1, 1, 12, 1] 73 rigid atoms, others: [32, 34, 12, 13, 14, 15, 16, 17, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 226 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220893 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)F)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 35, 35, 35, 35, 65, 65, 35, 35, 1, 2, 2, 2, 3, 3, 1, 11, 11, 35, 35, 65, 35] 73 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 229 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220893 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220893 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220893/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220893 Building REAL300000220894 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220894' /scratch/stefan/7769890/working/building/REAL300000220894 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220894 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220894/0 /scratch/stefan/7769890/working/building/REAL300000220894 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/908 `/scratch/stefan/7769890/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC(F)=C2C)N1) `REAL300000220894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220894 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC(F)=C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 15, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [27, 27, 27, 27, 37, 37, 37, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 37, 37, 9, 9, 1, 1, 2, 2, 2, 27] 37 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 109 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: REAL300000220894 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC(F)=C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 15, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 11, 11, 27, 27, 27, 27, 27, 1] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 71 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220894 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220894 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220894/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220894 Building REAL300000220895 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220895' /scratch/stefan/7769890/working/building/REAL300000220895 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220895 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220895/0 /scratch/stefan/7769890/working/building/REAL300000220895 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/909 `/scratch/stefan/7769890/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)[O-])S2)=N1) `REAL300000220895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220895 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)[O-])S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [27, 27, 27, 27, 35, 35, 35, 27, 27, 27, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 35, 35, 27, 11, 11, 1, 1] 35 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 96 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: REAL300000220895 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)[O-])S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 1, 11, 11, 27, 27] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220895 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220895 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220895/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220895 Building REAL300000220896 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220896' /scratch/stefan/7769890/working/building/REAL300000220896 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220896 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220896/0 /scratch/stefan/7769890/working/building/REAL300000220896 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/910 `/scratch/stefan/7769890/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=NC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1) `REAL300000220896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220896 none CCOC(=O)C1=NC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 136, 136, 80, 136, 80, 80, 80, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 80, 167, 167, 167, 167, 167, 80, 11, 11, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 482 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220896 none CCOC(=O)C1=NC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 7, 1, 7, 1, 1, 1, 1, 1, 12, 12, 80, 80, 80, 80, 80, 121, 146, 146, 80, 80, 80, 1, 21, 21, 21, 21, 21, 1, 12, 12, 81, 81, 81, 121, 121, 80] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 23, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 522 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220896 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220896 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220896/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220896 Building REAL300000220897 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220897' /scratch/stefan/7769890/working/building/REAL300000220897 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220897 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220897/0 /scratch/stefan/7769890/working/building/REAL300000220897 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/911 `/scratch/stefan/7769890/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(F)C=C1Br) `REAL300000220897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220897 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(F)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [77, 58, 58, 58, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 58, 58, 58, 58, 58, 77, 77, 77, 58, 12, 12, 2, 2, 2, 3, 3, 1, 58] 93 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 140 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220897 none COC1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C(F)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 11, 11, 58, 58, 58, 58, 58, 89, 93, 93, 58, 58, 58, 1, 1, 1, 1, 1, 4, 4, 4, 1, 11, 11, 58, 58, 58, 89, 89, 58, 1] 93 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 36, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 290 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220897 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220897 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220897/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220897 Building REAL300000220898 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220898' /scratch/stefan/7769890/working/building/REAL300000220898 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220898 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220898/0 /scratch/stefan/7769890/working/building/REAL300000220898 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/912 `/scratch/stefan/7769890/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Br)=C2Cl)=N1) `REAL300000220898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220898 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Br)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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: [28, 28, 28, 28, 36, 36, 36, 28, 28, 28, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 36, 36, 28, 7, 7, 1, 1, 1] 36 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 90 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: REAL300000220898 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(Br)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 28, 28, 25, 28, 28, 28, 28, 1, 2, 2, 2, 3, 3, 1, 11, 11, 28, 28, 28] 36 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 84 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220898 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220898 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220898/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220898 Building REAL300000220899 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220899' /scratch/stefan/7769890/working/building/REAL300000220899 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220899 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220899/0 /scratch/stefan/7769890/working/building/REAL300000220899 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/913 `/scratch/stefan/7769890/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C=CC(=O)[O-])C=C2)N1) `REAL300000220899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220899 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C=CC(=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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: [18, 18, 18, 18, 30, 36, 36, 18, 18, 18, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 1, 1, 18, 18, 18, 18, 30, 30, 3, 3, 1, 1, 5, 5, 1, 1, 18] 53 rigid atoms, others: [32, 33, 36, 37, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38]) total number of confs: 158 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: REAL300000220899 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C=CC(=O)[O-])C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 18, 18, 11, 11, 31, 31, 39, 41, 18, 18, 1, 2, 2, 2, 3, 3, 11, 11, 18, 18, 31, 31, 18, 18, 1] 53 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 24] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 170 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220899 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220899 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220899/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220899 Building REAL300000220900 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220900' /scratch/stefan/7769890/working/building/REAL300000220900 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220900 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220900/0 /scratch/stefan/7769890/working/building/REAL300000220900 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/914 `/scratch/stefan/7769890/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=C(C(=O)[O-])C=C2F)=N1) `REAL300000220900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220900 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=C(C(=O)[O-])C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [35, 35, 35, 35, 49, 78, 78, 35, 35, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 35, 35, 35, 35, 49, 49, 35, 11, 11, 1, 1] 78 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 262 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220900 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(F)=C(C(=O)[O-])C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 3, 6, 6, 1, 1, 1, 1, 1, 10, 10, 35, 35, 35, 35, 35, 58, 58, 35, 35, 35, 1, 2, 2, 2, 3, 3, 1, 10, 10, 35, 35] 78 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 171 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220900 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220900 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220900/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220900 Building REAL300000220901 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220901' /scratch/stefan/7769890/working/building/REAL300000220901 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220901 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220901/0 /scratch/stefan/7769890/working/building/REAL300000220901 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/915 `/scratch/stefan/7769890/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(F)=C2OC(F)(F)F)=N1) `REAL300000220901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220901 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(F)=C2OC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 102, 156, 156, 65, 65, 65, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 65, 65, 65, 65, 102, 102, 65, 9, 9, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 586 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220901 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(F)=C2OC(F)(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 65, 65, 65, 65, 65, 65, 65, 170, 185, 185, 185, 1, 2, 2, 2, 3, 3, 1, 11, 11, 65, 65, 65] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 359 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220901 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220901 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220901/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220901 Building REAL300000220902 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220902' /scratch/stefan/7769890/working/building/REAL300000220902 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220902 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220902/0 /scratch/stefan/7769890/working/building/REAL300000220902 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/916 `/scratch/stefan/7769890/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=CC=C2OC(C)C)N1) `REAL300000220902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220902 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=CC=C2OC(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 117, 156, 156, 67, 67, 67, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 15, 15, 67, 67, 67, 67, 117, 117, 9, 9, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 67] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 580 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220902 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(F)=CC=C2OC(C)C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 67, 67, 67, 30, 67, 67, 67, 130, 147, 147, 1, 2, 2, 2, 3, 3, 12, 12, 67, 29, 67, 147, 147, 147, 147, 147, 147, 147, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 42] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 393 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220902 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220902 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220902/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220902 Building REAL300000220903 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220903' /scratch/stefan/7769890/working/building/REAL300000220903 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220903 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220903/0 /scratch/stefan/7769890/working/building/REAL300000220903 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/917 `/scratch/stefan/7769890/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(F)=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000220903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220903 none CCOC1=CC(F)=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', '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, 15, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 117, 45, 45, 45, 45, 45, 45, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 45, 141, 141, 141, 141, 141, 45, 45, 12, 12, 3, 3, 2, 2, 2, 1, 45] 201 rigid atoms, others: [38, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 335 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: REAL300000220903 none CCOC1=CC(F)=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', '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, 15, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 45, 45, 45, 45, 45, 80, 124, 124, 45, 45, 45, 1, 13, 13, 13, 13, 13, 1, 1, 6, 6, 80, 80, 45, 45, 45, 45, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 39, 23, 29, 30] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 484 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220903 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220903 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220903/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220903 Building REAL300000220904 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220904' /scratch/stefan/7769890/working/building/REAL300000220904 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220904 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220904/0 /scratch/stefan/7769890/working/building/REAL300000220904 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/918 `/scratch/stefan/7769890/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)N3CCCC3)C=C2)=N1) `REAL300000220904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220904 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)N3CCCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 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, 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: [23, 23, 23, 23, 39, 52, 52, 23, 23, 23, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 22, 1, 1, 23, 23, 23, 23, 39, 39, 23, 4, 4, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1] 92 rigid atoms, others: [45, 35, 36, 12, 13, 14, 15, 16, 17, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 217 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220904 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)N3CCCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 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, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 23, 23, 11, 11, 64, 64, 67, 67, 67, 67, 23, 23, 1, 2, 2, 2, 3, 3, 1, 11, 11, 23, 23, 67, 67, 67, 67, 67, 67, 67, 67, 23, 23] 92 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 231 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220904 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(=O)N3CCCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 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, 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: [67, 67, 67, 67, 92, 92, 92, 67, 67, 67, 33, 33, 17, 13, 22, 22, 7, 1, 7, 1, 1, 1, 1, 1, 22, 22, 67, 67, 67, 67, 92, 92, 67, 33, 33, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 92 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46]) total number of confs: 325 number of broken/clashed sets: 92 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220904 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220904 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220904/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220904 Building REAL300000220905 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220905' /scratch/stefan/7769890/working/building/REAL300000220905 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220905 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220905/0 /scratch/stefan/7769890/working/building/REAL300000220905 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/919 `/scratch/stefan/7769890/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C=C2F)=N1) `REAL300000220905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220905 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 43, 75, 75, 29, 29, 29, 7, 7, 1, 1, 1, 1, 1, 1, 11, 23, 23, 1, 1, 1, 29, 29, 29, 29, 43, 43, 29, 7, 7, 1, 1, 23, 1] 201 rigid atoms, others: [33, 34, 36, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 318 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220905 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(OC(F)F)C=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 29, 29, 13, 29, 91, 145, 145, 29, 29, 29, 1, 2, 2, 2, 3, 3, 1, 9, 9, 29, 29, 145, 29] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 510 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220905 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220905 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220905/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220905 Building REAL300000220906 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220906' /scratch/stefan/7769890/working/building/REAL300000220906 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220906 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220906/0 /scratch/stefan/7769890/working/building/REAL300000220906 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/920 `/scratch/stefan/7769890/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(C)(C)C)=C2)=N1) `REAL300000220906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220906 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(C)(C)C)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 67, 101, 101, 38, 38, 38, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 1, 38, 38, 38, 38, 67, 67, 38, 6, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1] 163 rigid atoms, others: [33, 34, 35, 45, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 378 number of broken/clashed sets: 163 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220906 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC(C)(C)C)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 38, 38, 38, 38, 38, 81, 116, 116, 116, 38, 1, 2, 2, 2, 3, 3, 1, 11, 11, 38, 38, 38, 116, 116, 116, 116, 116, 116, 116, 116, 116, 38] 163 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 367 number of broken/clashed sets: 163 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220906 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220906 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220906/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220906 Building REAL300000220907 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220907' /scratch/stefan/7769890/working/building/REAL300000220907 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220907 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220907/0 /scratch/stefan/7769890/working/building/REAL300000220907 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/921 `/scratch/stefan/7769890/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(Cl)=C2C)N1) `REAL300000220907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220907 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(Cl)=C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [29, 29, 29, 29, 43, 43, 43, 29, 29, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 43, 43, 8, 8, 1, 1, 1, 2, 2, 2, 29] 43 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 135 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: REAL300000220907 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(Cl)=C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 29, 29, 29, 29, 29, 29, 29, 1, 2, 2, 2, 3, 3, 12, 12, 29, 29, 29, 29, 29, 29, 1] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220907 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220907 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220907/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220907 Building REAL300000220908 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220908' /scratch/stefan/7769890/working/building/REAL300000220908 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220908 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220908/0 /scratch/stefan/7769890/working/building/REAL300000220908 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/922 `/scratch/stefan/7769890/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C(F)C=C1C) `REAL300000220908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220908 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [67, 53, 53, 53, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 53, 53, 53, 53, 53, 67, 67, 67, 53, 12, 12, 3, 3, 2, 2, 2, 1, 53, 53, 53, 53] 85 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 125 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: REAL300000220908 none COC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 11, 11, 53, 53, 53, 53, 53, 75, 85, 85, 53, 53, 53, 1, 1, 1, 1, 1, 3, 3, 3, 1, 11, 11, 75, 75, 53, 53, 53, 45, 1, 2, 2, 2] 85 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 36, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 264 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220908 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220908 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220908/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220908 Building REAL300000220909 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220909' /scratch/stefan/7769890/working/building/REAL300000220909 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220909 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220909/0 /scratch/stefan/7769890/working/building/REAL300000220909 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/923 `/scratch/stefan/7769890/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(C)=C1Br) `REAL300000220909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220909 none CC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(C)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.3', 'C.ar', 'Br', '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, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 1, 17, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [17, 17, 17, 17, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 2, 2, 2, 3, 3, 1, 17, 17, 17] 31 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 58 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: REAL300000220909 none CC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(C)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.3', 'C.ar', 'Br', '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, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 1, 17, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 31, 31, 31, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 7, 17, 17, 17, 31, 31, 17, 2, 2, 2] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220909 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220909 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220909/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220909 Building REAL300000220910 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220910' /scratch/stefan/7769890/working/building/REAL300000220910 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220910 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220910/0 /scratch/stefan/7769890/working/building/REAL300000220910 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/924 `/scratch/stefan/7769890/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC2=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=CN=C12) `REAL300000220910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220910 none COC(=O)C1=CC=CC2=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 59, 146, 59, 59, 59, 59, 59, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 59, 59, 59, 59, 146, 146, 146, 59, 59, 59, 12, 12, 3, 3, 2, 2, 2, 1, 59, 59] 166 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 345 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: REAL300000220910 none COC(=O)C1=CC=CC2=C(C=CC3=NC(=O)C(CC(=O)[O-])=C(C)N3)C=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 10, 10, 59, 59, 59, 59, 59, 91, 140, 140, 59, 59, 59, 1, 1, 1, 1, 12, 12, 12, 1, 1, 1, 10, 10, 91, 91, 59, 59, 59, 55, 1, 1] 166 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 43, 24, 25, 26, 27, 42, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 497 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220910 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220910 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220910/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220910 Building REAL300000220911 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220911' /scratch/stefan/7769890/working/building/REAL300000220911 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220911 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220911/0 /scratch/stefan/7769890/working/building/REAL300000220911 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/925 `/scratch/stefan/7769890/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3C(=CC=C2)NN=C3C(=O)[O-])N1) `REAL300000220911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220911 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3C(=CC=C2)NN=C3C(=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 4, 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, 16, 21, 25, 25, 16, 16, 16, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 16, 16, 16, 21, 21, 7, 7, 1, 1, 1, 1, 16] 25 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 79 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: REAL300000220911 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3C(=CC=C2)NN=C3C(=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 19, 19, 1, 2, 2, 2, 3, 3, 11, 11, 16, 16, 16, 16, 1] 25 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 25] set([4, 5, 6, 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: 70 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220911 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220911 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220911/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220911 Building REAL300000220912 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220912' /scratch/stefan/7769890/working/building/REAL300000220912 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220912 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220912/0 /scratch/stefan/7769890/working/building/REAL300000220912 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/926 `/scratch/stefan/7769890/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)N1) `REAL300000220912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220912 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 81, 116, 116, 49, 49, 49, 11, 11, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 1, 6, 6, 1, 6, 6, 49, 50, 50, 50, 81, 81, 11, 11, 1, 6, 6, 6, 6, 1, 6, 6, 49] 201 rigid atoms, others: [36, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 449 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220912 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 49, 49, 49, 120, 128, 128, 49, 49, 49, 81, 81, 49, 81, 81, 1, 2, 2, 2, 3, 3, 11, 11, 49, 120, 120, 81, 81, 49, 81, 81, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 44, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 575 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220912 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 129, 161, 161, 81, 81, 81, 27, 27, 6, 6, 6, 6, 6, 23, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 129, 129, 27, 27, 6, 23, 23, 1, 1, 1, 1, 1, 81] 201 rigid atoms, others: [39, 40, 41, 42, 43, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44]) total number of confs: 644 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220912 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220912 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220912/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220912 Building REAL300000220913 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220913' /scratch/stefan/7769890/working/building/REAL300000220913 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220913 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220913/0 /scratch/stefan/7769890/working/building/REAL300000220913 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/927 `/scratch/stefan/7769890/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3CCCO3)N=N2)=N1) `REAL300000220913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220913 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3CCCO3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 64, 80, 80, 45, 45, 45, 7, 7, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 1, 1, 44, 45, 45, 45, 64, 64, 45, 8, 7, 1, 8, 8, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [33, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 321 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220913 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3CCCO3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 11, 11, 44, 44, 44, 114, 153, 153, 153, 153, 44, 44, 1, 2, 2, 2, 3, 3, 1, 11, 11, 45, 114, 114, 153, 153, 153, 153, 153, 153, 153] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 531 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220913 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3CCCO3)N=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 153, 201, 201, 201, 153, 153, 153, 53, 53, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 23, 23, 153, 153, 153, 153, 201, 201, 153, 53, 53, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 549 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220913 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220913 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220913/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220913 Building REAL300000220914 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220914' /scratch/stefan/7769890/working/building/REAL300000220914 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220914 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220914/0 /scratch/stefan/7769890/working/building/REAL300000220914 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/928 `/scratch/stefan/7769890/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N=N1) `REAL300000220914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220914 none CCCN1C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 136, 55, 55, 55, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 54, 55, 160, 160, 160, 160, 160, 136, 136, 55, 12, 12, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 596 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220914 none CCCN1C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 9, 1, 1, 1, 1, 1, 12, 12, 55, 55, 55, 54, 54, 82, 118, 118, 55, 55, 55, 1, 1, 17, 17, 17, 17, 17, 9, 9, 1, 12, 13, 55, 55, 55, 82, 82, 55] 201 rigid atoms, others: [2, 3, 4, 5, 6, 20, 21, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 456 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220914 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220914 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220914/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220914 Building REAL300000220915 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220915' /scratch/stefan/7769890/working/building/REAL300000220915 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220915 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220915/0 /scratch/stefan/7769890/working/building/REAL300000220915 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/929 `/scratch/stefan/7769890/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C=CC=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C) `REAL300000220915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220915 none CC1=CC(C)=C(C=CC=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 28, 60, 60, 60, 28, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 28, 28, 11, 11, 2, 2, 2, 3, 3, 1, 60, 60, 60, 60] 93 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 378 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220915 none CC1=CC(C)=C(C=CC=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 23, 23, 60, 60, 60, 60, 60, 93, 93, 93, 60, 60, 60, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 9, 9, 23, 23, 60, 60, 60, 93, 93, 60, 1, 2, 2, 2] 93 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 22, 23, 24, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 333 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220915 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220915 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220915/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220915 Building REAL300000220916 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220916' /scratch/stefan/7769890/working/building/REAL300000220916 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220916 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220916/0 /scratch/stefan/7769890/working/building/REAL300000220916 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/930 `/scratch/stefan/7769890/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC(F)=CC=C2F)N1) `REAL300000220916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220916 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC(F)=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 64, 110, 127, 127, 63, 64, 64, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 7, 9, 9, 9, 64, 64, 64, 64, 110, 110, 10, 10, 1, 2, 2, 2, 9, 7, 9, 64] 201 rigid atoms, others: [35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 451 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220916 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC(F)=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 64, 64, 64, 64, 64, 64, 126, 126, 126, 126, 126, 126, 126, 1, 2, 2, 2, 3, 3, 11, 11, 64, 64, 64, 64, 126, 126, 126, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 27, 42] set([4, 5, 6, 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, 41]) total number of confs: 208 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220916 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2C2=CC(F)=CC=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 126, 201, 201, 201, 126, 126, 126, 50, 50, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 201, 201, 50, 50, 9, 9, 9, 9, 1, 1, 1, 126] 201 rigid atoms, others: [39, 40, 41, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42]) total number of confs: 664 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220916 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220916 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220916/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220916 Building REAL300000220917 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220917' /scratch/stefan/7769890/working/building/REAL300000220917 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220917 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220917/0 /scratch/stefan/7769890/working/building/REAL300000220917 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/931 `/scratch/stefan/7769890/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=NC=C2Cl)=N1) `REAL300000220917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220917 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=NC=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 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: [19, 19, 19, 19, 21, 21, 21, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 21, 21, 19, 5, 5, 1, 1] 21 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 41 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: REAL300000220917 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C(Cl)C=NC=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 17, 17, 17, 14, 17, 17, 17, 1, 2, 2, 2, 3, 3, 1, 11, 11, 17, 17] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 67 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220917 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220917 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220917/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220917 Building REAL300000220918 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220918' /scratch/stefan/7769890/working/building/REAL300000220918 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220918 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220918/0 /scratch/stefan/7769890/working/building/REAL300000220918 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/932 `/scratch/stefan/7769890/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C=CC=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(C)=C1) `REAL300000220918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220918 none CC1=CC(C)=C(C=CC=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 22, 22, 22, 22, 22, 22, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 2, 2, 2, 3, 3, 1, 22, 22, 22, 22] 37 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 80 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: REAL300000220918 none CC1=CC(C)=C(C=CC=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 5, 5, 6, 6, 22, 22, 22, 22, 22, 37, 37, 37, 22, 22, 22, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 5, 6, 6, 22, 22, 22, 37, 37, 22, 2, 2, 2, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 45, 22, 23, 24, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 143 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220918 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220918 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220918/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220918 Building REAL300000220919 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220919' /scratch/stefan/7769890/working/building/REAL300000220919 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220919 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220919/0 /scratch/stefan/7769890/working/building/REAL300000220919 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/933 `/scratch/stefan/7769890/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=C2C(=O)NC3=C(Cl)C=CC(Cl)=C23)N1) `REAL300000220919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220919 none CC1=C(CC(=O)[O-])C(=O)N=C(C=C2C(=O)NC3=C(Cl)C=CC(Cl)=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 11, 8, 1, 1, 16, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [9, 9, 9, 9, 11, 11, 11, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 11, 11, 1, 1, 1, 1, 9] 11 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 24, 25, 26, 27, 28, 29]) total number of confs: 22 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: REAL300000220919 none CC1=C(CC(=O)[O-])C(=O)N=C(C=C2C(=O)NC3=C(Cl)C=CC(Cl)=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 11, 8, 1, 1, 16, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 3, 3, 9, 9, 9, 9, 1] 11 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 24] set([4, 5, 6, 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: 42 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220919 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220919 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220919/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220919 Building REAL300000220920 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220920' /scratch/stefan/7769890/working/building/REAL300000220920 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220920 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220920/0 /scratch/stefan/7769890/working/building/REAL300000220920 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/934 `/scratch/stefan/7769890/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3CC3)C=N2)N1) `REAL300000220920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220920 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3CC3)C=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 45, 45, 70, 85, 85, 45, 45, 45, 12, 12, 1, 1, 1, 1, 1, 13, 13, 1, 1, 46, 46, 46, 46, 70, 70, 12, 12, 1, 13, 13, 13, 13, 13, 1, 46] 135 rigid atoms, others: [35, 12, 13, 14, 15, 16, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 36]) total number of confs: 302 number of broken/clashed sets: 134 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220920 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3CC3)C=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 45, 45, 46, 97, 97, 45, 45, 1, 2, 2, 2, 3, 3, 11, 11, 46, 97, 97, 97, 97, 97, 45, 1] 136 rigid atoms, others: [0, 1, 2, 3, 36, 7, 8, 9, 10, 11, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 242 number of broken/clashed sets: 135 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220920 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C3CC3)C=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 135, 135, 135, 95, 95, 95, 56, 56, 13, 13, 13, 1, 1, 1, 1, 13, 13, 95, 95, 95, 95, 135, 135, 56, 56, 13, 1, 1, 1, 1, 1, 13, 95] 135 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 422 number of broken/clashed sets: 134 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220920 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220920 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220920/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220920 Building REAL300000220921 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220921' /scratch/stefan/7769890/working/building/REAL300000220921 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220921 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220921/0 /scratch/stefan/7769890/working/building/REAL300000220921 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/935 `/scratch/stefan/7769890/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O2)=N1) `REAL300000220921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220921 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [46, 45, 46, 46, 67, 83, 83, 46, 46, 46, 10, 10, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 21, 21, 12, 12, 12, 1, 45, 46, 46, 46, 67, 67, 46, 10, 10, 1, 1, 12, 12, 24, 12] 402 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 327 number of broken/clashed sets: 400 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220921 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 46, 46, 46, 46, 164, 164, 164, 164, 172, 172, 164, 164, 164, 46, 1, 2, 2, 2, 3, 3, 1, 11, 11, 46, 46, 163, 164, 328, 164] 402 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 604 number of broken/clashed sets: 400 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220921 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [164, 163, 164, 164, 201, 201, 201, 164, 164, 164, 51, 51, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 12, 163, 164, 164, 164, 201, 201, 164, 51, 51, 12, 12, 1, 1, 2, 1] 402 rigid atoms, others: [39, 40, 42, 16, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 485 number of broken/clashed sets: 400 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220921 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220921 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220921/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220921 Building REAL300000220922 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220922' /scratch/stefan/7769890/working/building/REAL300000220922 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220922 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220922/0 /scratch/stefan/7769890/working/building/REAL300000220922 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/936 `/scratch/stefan/7769890/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)N=C2F)=N1) `REAL300000220922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220922 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)N=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 8, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [19, 19, 19, 19, 33, 33, 33, 19, 19, 19, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 33, 33, 19, 9, 9, 1, 1] 33 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 119 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: REAL300000220922 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Br)N=C2F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 17, 8, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 1, 9, 9, 19, 19] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 21, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220922 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220922 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220922/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220922 Building REAL300000220923 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220923' /scratch/stefan/7769890/working/building/REAL300000220923 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220923 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220923/0 /scratch/stefan/7769890/working/building/REAL300000220923 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/937 `/scratch/stefan/7769890/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220923 none CCCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [80, 54, 20, 20, 36, 36, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 36, 36, 80, 80, 80, 80, 80, 54, 54, 36, 36, 11, 11, 3, 3, 2, 2, 2, 1, 36, 36] 101 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 407 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: REAL300000220923 none CCCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', '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, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 1, 1, 1, 1, 1, 1, 6, 6, 36, 36, 36, 36, 36, 60, 92, 92, 36, 36, 36, 1, 1, 8, 8, 8, 7, 7, 4, 4, 1, 1, 6, 6, 60, 60, 36, 36, 36, 36, 1, 1] 101 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 41, 21, 22, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 354 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220923 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220923 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220923/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220923 Building REAL300000220924 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220924' /scratch/stefan/7769890/working/building/REAL300000220924 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220924 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220924/0 /scratch/stefan/7769890/working/building/REAL300000220924 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/938 `/scratch/stefan/7769890/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1) `REAL300000220924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220924 none COC(=O)C1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 54, 128, 54, 54, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 54, 54, 128, 128, 128, 54, 12, 12, 2, 2, 2, 3, 3, 1, 54] 156 rigid atoms, others: [34, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 318 number of broken/clashed sets: 155 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220924 none COC(=O)C1=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 6, 6, 54, 54, 54, 54, 54, 87, 111, 111, 54, 54, 54, 1, 1, 13, 13, 13, 1, 6, 6, 54, 54, 54, 87, 87, 54, 1] 156 rigid atoms, others: [2, 35, 4, 5, 6, 7, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 391 number of broken/clashed sets: 155 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220924 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220924 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220924/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220924 Building REAL300000220925 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220925' /scratch/stefan/7769890/working/building/REAL300000220925 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220925 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220925/0 /scratch/stefan/7769890/working/building/REAL300000220925 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/939 `/scratch/stefan/7769890/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(C(F)(F)F)=C1) `REAL300000220925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220925 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [117, 117, 43, 117, 43, 43, 43, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 43, 43, 43, 43, 43, 43, 117, 117, 117, 43, 43, 12, 12, 2, 2, 2, 3, 3, 1, 43] 140 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 305 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220925 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 5, 5, 43, 43, 43, 43, 43, 70, 100, 100, 43, 43, 43, 1, 1, 2, 2, 2, 1, 13, 13, 13, 1, 1, 5, 5, 43, 43, 43, 70, 70, 43, 1] 140 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 41, 22, 23, 27, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 369 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220925 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220925 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220925/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220925 Building REAL300000220926 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220926' /scratch/stefan/7769890/working/building/REAL300000220926 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220926 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220926/0 /scratch/stefan/7769890/working/building/REAL300000220926 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/940 `/scratch/stefan/7769890/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C3CSCCC3=NN2C)=N1) `REAL300000220926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220926 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C3CSCCC3=NN2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 5, 5, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 39, 39, 39, 49, 49, 49, 39, 39, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 49, 49, 36, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2] 49 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40]) total number of confs: 123 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: REAL300000220926 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C3CSCCC3=NN2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 5, 5, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 3, 3, 1, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 82 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220926 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220926 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220926/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220926 Building REAL300000220927 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220927' /scratch/stefan/7769890/working/building/REAL300000220927 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220927 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220927/0 /scratch/stefan/7769890/working/building/REAL300000220927 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/941 `/scratch/stefan/7769890/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C2=CC=CC=C2)=N1) `REAL300000220927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220927 none CCN1C=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', '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, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 61, 61, 61, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 62, 62, 84, 84, 62, 84, 84, 61, 107, 107, 107, 107, 107, 62, 11, 11, 3, 3, 2, 2, 2, 1, 84, 84, 62, 84, 84] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 40] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 463 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220927 none CCN1C=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', '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, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 11, 11, 61, 61, 62, 61, 61, 106, 161, 161, 62, 62, 62, 1, 1, 6, 6, 1, 6, 6, 1, 8, 8, 8, 8, 8, 1, 11, 11, 106, 106, 62, 62, 62, 62, 6, 6, 1, 6, 6] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 611 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220927 none CCN1C=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', '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, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 6, 6, 6, 6, 6, 27, 27, 84, 84, 84, 84, 84, 134, 201, 201, 84, 84, 84, 1, 1, 1, 1, 1, 1, 1, 6, 23, 23, 23, 23, 23, 6, 27, 27, 134, 134, 84, 84, 84, 84, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 765 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220927 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220927 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220927/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220927 Building REAL300000220928 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220928' /scratch/stefan/7769890/working/building/REAL300000220928 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220928 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220928/0 /scratch/stefan/7769890/working/building/REAL300000220928 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/942 `/scratch/stefan/7769890/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2CCOC3)N1) `REAL300000220928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220928 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2CCOC3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 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: [30, 30, 30, 30, 42, 42, 42, 30, 30, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 42, 42, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28] 42 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 118 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: REAL300000220928 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2CCOC3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 30, 30, 19, 30, 30, 30, 30, 30, 30, 1, 2, 2, 2, 3, 3, 10, 10, 30, 30, 19, 30, 30, 30, 30, 30, 30, 1] 42 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 40, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220928 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220928 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220928/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220928 Building REAL300000220929 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220929' /scratch/stefan/7769890/working/building/REAL300000220929 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220929 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220929/0 /scratch/stefan/7769890/working/building/REAL300000220929 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/943 `/scratch/stefan/7769890/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=C(C)C=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1C) `REAL300000220929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220929 none COCC1=C(C)C=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 5, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [169, 143, 41, 41, 24, 41, 41, 41, 41, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 41, 41, 169, 169, 169, 143, 143, 41, 41, 41, 41, 41, 41, 41, 12, 12, 3, 3, 2, 2, 2, 1, 41, 41, 41] 197 rigid atoms, others: [45, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 607 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: REAL300000220929 none COCC1=C(C)C=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 5, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 41, 41, 73, 112, 112, 41, 41, 41, 1, 1, 22, 22, 22, 6, 6, 2, 2, 2, 1, 2, 2, 2, 7, 7, 73, 73, 41, 41, 41, 39, 2, 2, 2] 197 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 24, 25] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 463 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220929 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220929 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220929/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220929 Building REAL300000220930 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220930' /scratch/stefan/7769890/working/building/REAL300000220930 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220930 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220930/0 /scratch/stefan/7769890/working/building/REAL300000220930 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/944 `/scratch/stefan/7769890/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OC(=O)OC3=C2)N1) `REAL300000220930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220930 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OC(=O)OC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 3, 7, 7, 4, 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: [19, 19, 19, 19, 27, 27, 27, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 27, 27, 6, 6, 1, 1, 1, 19] 27 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 79 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: REAL300000220930 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OC(=O)OC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 9, 9, 19, 19, 19, 1] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 61 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220930 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220930 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220930/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220930 Building REAL300000220931 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220931' /scratch/stefan/7769890/working/building/REAL300000220931 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220931 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220931/0 /scratch/stefan/7769890/working/building/REAL300000220931 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/945 `/scratch/stefan/7769890/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1) `REAL300000220931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220931 none CC1=C(Br)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [25, 25, 25, 25, 25, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 25, 25, 25, 25, 25, 10, 10, 2, 2, 2, 3, 3, 1] 38 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 65 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: REAL300000220931 none CC1=C(Br)C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 9, 9, 25, 25, 25, 25, 25, 38, 38, 38, 25, 25, 25, 1, 2, 2, 2, 1, 9, 9, 25, 25, 25, 38, 38, 25] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 128 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220931 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220931 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220931/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220931 Building REAL300000220932 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220932' /scratch/stefan/7769890/working/building/REAL300000220932 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220932 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220932/0 /scratch/stefan/7769890/working/building/REAL300000220932 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/946 `/scratch/stefan/7769890/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)N1) `REAL300000220932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220932 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [30, 30, 30, 30, 53, 69, 69, 30, 30, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 30, 30, 30, 30, 53, 53, 6, 6, 1, 1, 1, 3, 3, 3, 3, 1, 30] 69 rigid atoms, others: [34, 35, 36, 41, 12, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 42]) total number of confs: 250 number of broken/clashed sets: 69 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220932 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 6, 6, 1, 1, 1, 1, 1, 10, 10, 30, 30, 30, 30, 30, 48, 48, 40, 48, 48, 48, 30, 1, 2, 2, 2, 3, 3, 10, 10, 30, 30, 30, 48, 48, 48, 48, 30, 1] 69 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 26, 42] set([4, 5, 6, 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, 41]) total number of confs: 151 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220932 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [48, 48, 48, 48, 69, 69, 69, 48, 48, 48, 10, 10, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 48, 48, 48, 48, 69, 69, 10, 10, 3, 3, 3, 1, 1, 1, 1, 3, 48] 69 rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 194 number of broken/clashed sets: 69 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220932 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220932 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220932/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220932 Building REAL300000220933 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220933' /scratch/stefan/7769890/working/building/REAL300000220933 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220933 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220933/0 /scratch/stefan/7769890/working/building/REAL300000220933 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/947 `/scratch/stefan/7769890/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=NC=CC=C23)N1) `REAL300000220933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220933 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=NC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [31, 31, 31, 31, 41, 41, 41, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 41, 41, 9, 9, 1, 1, 1, 1, 1, 1, 31] 41 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 105 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: REAL300000220933 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=NC=CC=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 9, 9, 31, 31, 31, 31, 31, 31, 1] 41 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 73 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220933 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220933 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220933/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220933 Building REAL300000220934 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220934' /scratch/stefan/7769890/working/building/REAL300000220934 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220934 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220934/0 /scratch/stefan/7769890/working/building/REAL300000220934 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/948 `/scratch/stefan/7769890/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2[N+](=O)[O-])N1) `REAL300000220934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220934 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2[N+](=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 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: [40, 40, 40, 40, 51, 51, 51, 40, 40, 40, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 51, 51, 10, 10, 1, 2, 2, 2, 40] 51 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 132 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: REAL300000220934 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(C)N=C2[N+](=O)[O-])N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 40, 40, 40, 40, 40, 40, 40, 40, 1, 2, 2, 2, 3, 3, 10, 10, 40, 40, 40, 40, 1] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 83 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220934 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220934 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220934/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220934 Building REAL300000220935 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220935' /scratch/stefan/7769890/working/building/REAL300000220935 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220935 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220935/0 /scratch/stefan/7769890/working/building/REAL300000220935 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/949 `/scratch/stefan/7769890/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C) `REAL300000220935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220935 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 111, 59, 27, 19, 28, 28, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 28, 28, 28, 146, 146, 146, 146, 146, 111, 111, 28, 28, 9, 9, 2, 2, 2, 3, 3, 1, 28, 28, 28, 28] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45]) total number of confs: 627 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220935 none CCCOC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 6, 1, 1, 1, 1, 1, 1, 5, 5, 28, 28, 28, 28, 28, 50, 89, 89, 28, 28, 28, 1, 1, 1, 25, 25, 25, 25, 25, 14, 14, 1, 1, 5, 5, 28, 28, 28, 50, 50, 28, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 42, 22, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 439 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220935 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220935 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220935/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220935 Building REAL300000220936 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220936' /scratch/stefan/7769890/working/building/REAL300000220936 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220936 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220936/0 /scratch/stefan/7769890/working/building/REAL300000220936 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/950 `/scratch/stefan/7769890/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=NC=CN=C3C=C2)N1) `REAL300000220936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220936 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=NC=CN=C3C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 28, 28, 28, 19, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 28, 28, 7, 7, 1, 1, 1, 1, 1, 19] 28 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 85 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: REAL300000220936 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC3=NC=CN=C3C=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 10, 10, 19, 19, 19, 19, 19, 1] 28 rigid atoms, others: [0, 1, 2, 3, 36, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 62 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220936 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220936 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220936/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220936 Building REAL300000220937 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220937' /scratch/stefan/7769890/working/building/REAL300000220937 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220937 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220937/0 /scratch/stefan/7769890/working/building/REAL300000220937 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/951 `/scratch/stefan/7769890/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1CN1C=CC=N1) `REAL300000220937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220937 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1CN1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 29, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 29, 29, 90, 130, 130, 130, 130, 51, 51, 51, 29, 29, 9, 9, 2, 2, 2, 3, 3, 1, 29, 90, 90, 130, 130, 130] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 495 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220937 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1CN1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 54, 79, 79, 29, 29, 29, 1, 1, 1, 5, 11, 11, 11, 11, 4, 4, 4, 1, 1, 5, 5, 29, 29, 29, 54, 54, 29, 1, 5, 5, 11, 11, 11] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 41, 20, 21, 22, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 321 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220937 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1CN1C=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 11, 11, 11, 11, 11, 39, 39, 130, 130, 130, 130, 130, 201, 201, 201, 130, 130, 130, 11, 5, 1, 1, 1, 1, 1, 1, 19, 19, 19, 11, 11, 39, 39, 130, 130, 130, 201, 201, 130, 11, 5, 5, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 661 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220937 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220937 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220937/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220937 Building REAL300000220938 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220938' /scratch/stefan/7769890/working/building/REAL300000220938 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220938 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220938/0 /scratch/stefan/7769890/working/building/REAL300000220938 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/952 `/scratch/stefan/7769890/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(F)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220938 none CCOC1=CC=CC(F)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 122, 63, 63, 63, 12, 63, 63, 63, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 159, 159, 159, 159, 159, 63, 61, 63, 12, 12, 3, 3, 2, 2, 2, 1] 201 rigid atoms, others: [39, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 554 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: REAL300000220938 none CCOC1=CC=CC(F)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 63, 63, 63, 63, 63, 105, 147, 147, 63, 63, 63, 27, 27, 27, 27, 27, 1, 1, 1, 9, 9, 105, 105, 63, 63, 63, 63] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 576 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220938 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220938 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220938/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220938 Building REAL300000220939 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220939' /scratch/stefan/7769890/working/building/REAL300000220939 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220939 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220939/0 /scratch/stefan/7769890/working/building/REAL300000220939 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/953 `/scratch/stefan/7769890/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Br)C(F)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220939 none CC1=CC=C(Br)C(F)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 15, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [33, 33, 33, 33, 33, 33, 33, 33, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 33, 33, 33, 33, 33, 10, 10, 2, 2, 2, 3, 3, 1] 41 rigid atoms, others: [35, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 74 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220939 none CC1=CC=C(Br)C(F)=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 15, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 1, 1, 9, 9, 33, 33, 33, 33, 33, 41, 41, 41, 33, 33, 33, 2, 2, 2, 1, 1, 9, 9, 33, 33, 33, 41, 41, 33] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27] set([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: 105 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220939 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220939 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220939/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220939 Building REAL300000220940 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220940' /scratch/stefan/7769890/working/building/REAL300000220940 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220940 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220940/0 /scratch/stefan/7769890/working/building/REAL300000220940 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/954 `/scratch/stefan/7769890/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC([N+](=O)[O-])=C2C)N1) `REAL300000220940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220940 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC([N+](=O)[O-])=C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 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: [31, 31, 31, 31, 41, 41, 41, 31, 31, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 31, 31, 31, 31, 41, 41, 9, 9, 1, 1, 1, 2, 2, 2, 30] 41 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 118 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: REAL300000220940 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC([N+](=O)[O-])=C2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 31, 31, 10, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 10, 10, 31, 31, 10, 31, 31, 31, 1] 41 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 116 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220940 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220940 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220940/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220940 Building REAL300000220941 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220941' /scratch/stefan/7769890/working/building/REAL300000220941 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220941 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220941/0 /scratch/stefan/7769890/working/building/REAL300000220941 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/955 `/scratch/stefan/7769890/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C([N+](=O)[O-])C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220941 none CC1=CC=C([N+](=O)[O-])C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 8, 11, 11, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [33, 33, 33, 11, 33, 33, 33, 33, 33, 33, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 33, 33, 33, 33, 22, 33, 33, 33, 11, 11, 3, 3, 2, 2, 2, 1] 39 rigid atoms, others: [40, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220941 none CC1=CC=C([N+](=O)[O-])C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 8, 11, 11, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 39, 39, 39, 33, 33, 33, 2, 2, 2, 1, 1, 2, 2, 2, 7, 7, 39, 39, 33, 33, 33, 31] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 28, 29] set([6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220941 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220941 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220941/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220941 Building REAL300000220942 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220942' /scratch/stefan/7769890/working/building/REAL300000220942 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220942 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220942/0 /scratch/stefan/7769890/working/building/REAL300000220942 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/956 `/scratch/stefan/7769890/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(S(N)(=O)=O)=C2)N1) `REAL300000220942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220942 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(S(N)(=O)=O)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 4, 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: [23, 23, 23, 23, 37, 37, 37, 23, 23, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 23, 23, 23, 23, 37, 37, 6, 6, 1, 1, 1, 5, 5, 1, 23] 129 rigid atoms, others: [32, 33, 36, 12, 13, 14, 15, 16, 17, 18, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 37]) total number of confs: 135 number of broken/clashed sets: 129 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220942 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(S(N)(=O)=O)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 23, 23, 16, 23, 23, 84, 84, 84, 23, 1, 2, 2, 2, 3, 3, 9, 9, 23, 23, 21, 84, 84, 23, 1] 129 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 341 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220942 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220942 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220942/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220942 Building REAL300000220943 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220943' /scratch/stefan/7769890/working/building/REAL300000220943 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220943 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220943/0 /scratch/stefan/7769890/working/building/REAL300000220943 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/957 `/scratch/stefan/7769890/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CN2C=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)N=N2)C=C1) `REAL300000220943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220943 none COC1=CC=C(CN2C=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 15, 15, 27, 27, 8, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 46, 72, 72, 29, 29, 29, 1, 1, 27, 27, 27, 27, 27, 27, 27, 8, 8, 1, 7, 7, 29, 29, 29, 46, 46, 29, 27, 27] 201 rigid atoms, others: [35, 6, 7, 8, 9, 10, 24, 25] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 359 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220943 none COC1=CC=C(CN2C=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 27, 27, 27, 51, 51, 155, 155, 155, 155, 155, 201, 201, 201, 155, 155, 155, 27, 27, 1, 1, 2, 2, 2, 1, 1, 6, 6, 27, 51, 51, 155, 155, 155, 201, 201, 155, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 44, 45, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 538 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220943 none COC1=CC=C(CN2C=C(C=CC3=NC(C)=C(CC(=O)[O-])C(=O)N3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 135, 135, 155, 155, 87, 29, 29, 29, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 29, 155, 155, 155, 155, 155, 155, 155, 87, 87, 29, 12, 12, 2, 2, 2, 3, 3, 1, 155, 155] 201 rigid atoms, others: [43, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 533 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220943 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220943 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220943/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220943 Building REAL300000220944 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220944' /scratch/stefan/7769890/working/building/REAL300000220944 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220944 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220944/0 /scratch/stefan/7769890/working/building/REAL300000220944 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/958 `/scratch/stefan/7769890/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(Cl)N2C)N1) `REAL300000220944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220944 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(Cl)N2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 16, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [25, 25, 25, 25, 43, 43, 43, 25, 25, 25, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 43, 43, 9, 9, 1, 2, 2, 2, 25] 43 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 155 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: REAL300000220944 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=C(Cl)N2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 16, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 25, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 3, 11, 11, 25, 25, 25, 25, 1] 43 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 20] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 67 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220944 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220944 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220944/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220944 Building REAL300000220945 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220945' /scratch/stefan/7769890/working/building/REAL300000220945 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220945 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220945/0 /scratch/stefan/7769890/working/building/REAL300000220945 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/959 `/scratch/stefan/7769890/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(F)=C1) `REAL300000220945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220945 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 66, 118, 23, 66, 66, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 66, 66, 66, 118, 118, 118, 66, 66, 12, 12, 2, 2, 2, 3, 3, 1, 66] 164 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 426 number of broken/clashed sets: 164 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220945 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 12, 12, 66, 66, 66, 66, 66, 104, 113, 113, 66, 66, 66, 1, 1, 1, 13, 13, 13, 1, 1, 12, 12, 66, 66, 66, 104, 104, 66, 1] 164 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 24, 38, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 383 number of broken/clashed sets: 164 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220945 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220945 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220945/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220945 Building REAL300000220946 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220946' /scratch/stefan/7769890/working/building/REAL300000220946 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220946 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220946/0 /scratch/stefan/7769890/working/building/REAL300000220946 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/960 `/scratch/stefan/7769890/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC3=CC=CC=N3)=C2)N1) `REAL300000220946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220946 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC3=CC=CC=N3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 33, 36, 36, 17, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 1, 17, 17, 17, 17, 33, 33, 5, 5, 1, 1, 1, 15, 15, 15, 15, 1, 17] 201 rigid atoms, others: [34, 35, 36, 41, 12, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 42]) total number of confs: 156 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220946 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC3=CC=CC=N3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 85, 115, 115, 115, 115, 115, 17, 1, 2, 2, 2, 3, 3, 6, 6, 17, 17, 17, 115, 115, 115, 115, 17, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 26, 42] set([4, 5, 6, 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, 41]) total number of confs: 196 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220946 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(OC3=CC=CC=N3)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 115, 201, 201, 201, 115, 115, 115, 51, 51, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 15, 115, 115, 115, 115, 201, 201, 51, 51, 15, 15, 15, 1, 1, 1, 1, 15, 115] 201 rigid atoms, others: [37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 741 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220946 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220946 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220946/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220946 Building REAL300000220947 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220947' /scratch/stefan/7769890/working/building/REAL300000220947 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220947 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220947/0 /scratch/stefan/7769890/working/building/REAL300000220947 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/961 `/scratch/stefan/7769890/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(COC3=CC=CC=C3)=C2)=N1) `REAL300000220947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220947 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(COC3=CC=CC=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 49, 76, 76, 28, 28, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 8, 8, 7, 8, 8, 1, 28, 28, 28, 28, 49, 49, 28, 5, 5, 1, 1, 1, 7, 7, 8, 8, 7, 8, 8, 1] 201 rigid atoms, others: [36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 298 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220947 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(COC3=CC=CC=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 28, 28, 17, 28, 28, 127, 127, 127, 127, 127, 127, 127, 28, 1, 2, 2, 2, 3, 3, 1, 9, 9, 28, 28, 23, 127, 127, 127, 127, 127, 127, 127, 28] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 484 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220947 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(COC3=CC=CC=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 201, 201, 201, 127, 127, 127, 29, 29, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 8, 127, 127, 127, 127, 201, 201, 127, 29, 29, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 8] 201 rigid atoms, others: [41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 636 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220947 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220947 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220947/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220947 Building REAL300000220948 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220948' /scratch/stefan/7769890/working/building/REAL300000220948 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220948 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220948/0 /scratch/stefan/7769890/working/building/REAL300000220948 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/962 `/scratch/stefan/7769890/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)=N1) `REAL300000220948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220948 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 14, 21, 21, 10, 10, 10, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1, 10, 10, 10, 10, 14, 14, 10, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1] 21 rigid atoms, others: [37, 38, 44, 43, 12, 13, 14, 15, 16, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 81 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: REAL300000220948 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 8, 8, 10, 10, 8, 10, 15, 15, 10, 11, 15, 15, 15, 15, 10, 10, 1, 2, 2, 2, 3, 3, 1, 8, 8, 10, 10, 15, 15, 15, 15, 10, 10] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 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: REAL300000220948 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 21, 21, 21, 15, 15, 15, 5, 5, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 15, 15, 15, 15, 21, 21, 15, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3] 21 rigid atoms, others: [39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 72 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220948 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220948 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220948/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220948 Building REAL300000220949 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220949' /scratch/stefan/7769890/working/building/REAL300000220949 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220949 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220949/0 /scratch/stefan/7769890/working/building/REAL300000220949 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/963 `/scratch/stefan/7769890/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC(F)F)=N1) `REAL300000220949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220949 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 58, 102, 102, 34, 34, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 27, 58, 58, 34, 34, 34, 34, 58, 58, 34, 9, 9, 1, 1, 1, 1, 27, 27, 58] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 595 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220949 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC=C2OCC(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 34, 34, 20, 34, 34, 34, 76, 117, 165, 165, 1, 2, 2, 2, 3, 3, 1, 9, 9, 34, 34, 34, 34, 117, 117, 165] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 648 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220949 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220949 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220949/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220949 Building REAL300000220950 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220950' /scratch/stefan/7769890/working/building/REAL300000220950 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000220950 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220950/0 /scratch/stefan/7769890/working/building/REAL300000220950 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/964 `/scratch/stefan/7769890/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([O-])C(F)=C2F)N1) `REAL300000220950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220950 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([O-])C(F)=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 15, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [29, 29, 29, 29, 43, 43, 43, 29, 29, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 43, 43, 11, 11, 1, 1, 29] 43 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 131 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: REAL300000220950 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C([O-])C(F)=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 15, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 1, 2, 2, 2, 3, 3, 11, 11, 29, 29, 1] 43 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 73 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220950 /scratch/stefan/7769890/working /scratch/stefan/7769890 mkdir: created directory `1' /scratch/stefan/7769890/working/building/REAL300000220950/1 /scratch/stefan/7769890/working/building/REAL300000220950 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/965 `/scratch/stefan/7769890/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C(F)=C2F)N1) `REAL300000220950.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000220950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220950/1/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: REAL300000220950 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C(F)=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 15, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 42, 42, 42, 35, 35, 35, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 42, 42, 10, 10, 1, 1, 2, 35] 84 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 97 number of broken/clashed sets: 84 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220950 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(O)C(F)=C2F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 15, 1, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 11, 11, 35, 35, 70, 1] 84 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 148 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220950 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220950 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 1: /scratch/stefan/7769890/working/building/REAL300000220950/1.* 0: /scratch/stefan/7769890/working/building/REAL300000220950/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220950 Building REAL300000220951 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220951' /scratch/stefan/7769890/working/building/REAL300000220951 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220951 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220951/0 /scratch/stefan/7769890/working/building/REAL300000220951 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/966 `/scratch/stefan/7769890/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)C=N2)N1) `REAL300000220951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220951 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)C=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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: [15, 15, 15, 15, 29, 29, 29, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 15, 16, 16, 16, 29, 29, 6, 6, 1, 1, 1, 15] 29 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 113 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: REAL300000220951 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(Cl)C=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 3, 8, 8, 15, 15, 15, 1] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 20, 31] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 55 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220951 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220951 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220951/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220951 Building REAL300000220952 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220952' /scratch/stefan/7769890/working/building/REAL300000220952 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220952 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220952/0 /scratch/stefan/7769890/working/building/REAL300000220952 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/967 `/scratch/stefan/7769890/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC=CC2=CC=CC(F)=C2)N1) `REAL300000220952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220952 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC=CC2=CC=CC(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [55, 55, 55, 55, 73, 73, 73, 55, 55, 55, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 73, 73, 15, 15, 6, 6, 1, 1, 1, 1, 55] 73 rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 199 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220952 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC=CC2=CC=CC(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 13, 13, 27, 27, 55, 55, 55, 55, 55, 55, 1, 2, 2, 2, 3, 3, 13, 13, 27, 27, 55, 55, 55, 55, 1] 73 rigid atoms, others: [0, 1, 2, 3, 36, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 147 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220952 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220952 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220952/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220952 Building REAL300000220953 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220953' /scratch/stefan/7769890/working/building/REAL300000220953 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220953 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220953/0 /scratch/stefan/7769890/working/building/REAL300000220953 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/968 `/scratch/stefan/7769890/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CNC(Br)=C2)=N1) `REAL300000220953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220953 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CNC(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 4, 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: [21, 21, 21, 21, 27, 27, 27, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 21, 22, 22, 22, 27, 27, 22, 6, 6, 1, 1, 1] 27 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 75 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: REAL300000220953 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CNC(Br)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 17, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 1, 11, 11, 22, 21, 21] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 19, 25] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 64 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220953 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220953 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220953/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220953 Building REAL300000220954 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220954' /scratch/stefan/7769890/working/building/REAL300000220954 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220954 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220954/0 /scratch/stefan/7769890/working/building/REAL300000220954 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/969 `/scratch/stefan/7769890/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(F)=C1OC) `REAL300000220954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220954 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(F)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'F', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 78, 78, 78, 78, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 78, 78, 78, 78, 148, 142, 142, 142, 78, 78, 11, 11, 2, 2, 2, 3, 3, 1, 148, 148, 148] 201 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 361 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220954 none COC1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(F)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'F', 'C.ar', 'O.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, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 11, 11, 78, 78, 78, 78, 78, 127, 152, 152, 78, 78, 78, 1, 1, 1, 1, 6, 4, 4, 4, 1, 1, 11, 11, 78, 78, 78, 127, 127, 78, 6, 6, 6] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 509 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220954 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220954 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220954/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220954 Building REAL300000220955 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220955' /scratch/stefan/7769890/working/building/REAL300000220955 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220955 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220955/0 /scratch/stefan/7769890/working/building/REAL300000220955 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/970 `/scratch/stefan/7769890/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2C)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220955 none CC1=NN(C2=CC=CC=C2C)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 38, 38, 94, 94, 94, 94, 94, 121, 121, 121, 94, 94, 94, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 38, 38, 121, 121, 94, 94, 94, 94] 121 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 325 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: REAL300000220955 none CC1=NN(C2=CC=CC=C2C)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 1, 1, 1, 1, 9, 9, 46, 46, 46, 46, 46, 67, 72, 72, 46, 46, 46, 2, 2, 2, 7, 7, 1, 7, 7, 7, 7, 2, 2, 2, 9, 9, 67, 67, 46, 46, 46, 46] 121 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 235 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220955 none CC1=NN(C2=CC=CC=C2C)C(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 46, 94, 94, 64, 94, 94, 94, 46, 46, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 46, 46, 46, 94, 94, 46, 94, 94, 94, 94, 46, 46, 46, 12, 12, 3, 3, 2, 2, 2, 1] 121 rigid atoms, others: [48, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 264 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220955 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220955 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220955/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220955 Building REAL300000220956 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220956' /scratch/stefan/7769890/working/building/REAL300000220956 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220956 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220956/0 /scratch/stefan/7769890/working/building/REAL300000220956 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/971 `/scratch/stefan/7769890/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNC3=CC=C(C(=O)[O-])C=C23)N1) `REAL300000220956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220956 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNC3=CC=C(C(=O)[O-])C=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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, 38, 38, 38, 47, 47, 47, 37, 38, 37, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 38, 38, 38, 47, 47, 12, 12, 1, 1, 1, 1, 1, 38] 47 rigid atoms, others: [33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 119 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220956 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CNC3=CC=C(C(=O)[O-])C=C23)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 2, 2, 2, 3, 3, 9, 9, 38, 38, 38, 38, 38, 1] 47 rigid atoms, others: [0, 1, 2, 3, 38, 7, 8, 9, 10, 11, 25] set([4, 5, 6, 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: 78 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220956 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220956 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220956/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220956 Building REAL300000220957 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220957' /scratch/stefan/7769890/working/building/REAL300000220957 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220957 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220957/0 /scratch/stefan/7769890/working/building/REAL300000220957 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/972 `/scratch/stefan/7769890/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(=O)[O-])N=C2)N1) `REAL300000220957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220957 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(=O)[O-])N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 26, 26, 26, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 26, 26, 5, 5, 1, 1, 1, 22] 26 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 57 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: REAL300000220957 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(=O)[O-])N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 11, 11, 22, 22, 22, 1] 26 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 63 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220957 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220957 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220957/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220957 Building REAL300000220958 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220958' /scratch/stefan/7769890/working/building/REAL300000220958 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220958 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220958/0 /scratch/stefan/7769890/working/building/REAL300000220958 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/973 `/scratch/stefan/7769890/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(=O)[O-])C(O)=C2)N1) `REAL300000220958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220958 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(=O)[O-])C(O)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 36, 46, 46, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 21, 21, 21, 21, 36, 36, 6, 6, 1, 1, 2, 1, 21] 92 rigid atoms, others: [32, 34, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 35]) total number of confs: 171 number of broken/clashed sets: 92 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220958 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C(C(=O)[O-])C(O)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 3, 7, 7, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 21, 27, 27, 21, 21, 21, 1, 2, 2, 2, 3, 3, 8, 8, 21, 21, 42, 21, 1] 92 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 130 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220958 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220958 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220958/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220958 Building REAL300000220959 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220959' /scratch/stefan/7769890/working/building/REAL300000220959 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220959 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220959/0 /scratch/stefan/7769890/working/building/REAL300000220959 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/974 `/scratch/stefan/7769890/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C) `REAL300000220959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220959 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 36, 110, 36, 36, 36, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 36, 36, 36, 110, 110, 110, 36, 36, 12, 12, 2, 2, 2, 3, 3, 1, 36, 36, 36, 36] 120 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 285 number of broken/clashed sets: 120 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220959 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', '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, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 63, 80, 80, 36, 36, 36, 1, 1, 1, 13, 13, 13, 1, 1, 7, 7, 36, 36, 36, 63, 63, 36, 1, 2, 2, 2] 120 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 24, 38, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 311 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220959 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220959 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220959/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220959 Building REAL300000220960 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220960' /scratch/stefan/7769890/working/building/REAL300000220960 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220960 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220960/0 /scratch/stefan/7769890/working/building/REAL300000220960 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/975 `/scratch/stefan/7769890/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C(=O)[O-]) `REAL300000220960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220960 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 2, 2, 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: [32, 32, 32, 32, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 32, 32, 32, 47, 47, 32, 32, 32, 32, 32, 12, 12, 3, 3, 2, 2, 2, 1, 32] 64 rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 141 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: REAL300000220960 none CC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 2, 2, 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, 1, 1, 1, 6, 6, 32, 32, 32, 32, 32, 50, 64, 64, 32, 32, 32, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 6, 6, 50, 50, 32, 32, 32, 32, 1] 64 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 27, 28, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 221 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220960 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220960 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220960/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220960 Building REAL300000220961 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220961' /scratch/stefan/7769890/working/building/REAL300000220961 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220961 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220961/0 /scratch/stefan/7769890/working/building/REAL300000220961 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/976 `/scratch/stefan/7769890/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(=O)[O-])=C(Cl)S2)=N1) `REAL300000220961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220961 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(=O)[O-])=C(Cl)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [54, 54, 54, 54, 64, 82, 82, 54, 54, 54, 11, 11, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 54, 54, 54, 54, 64, 64, 54, 11, 11, 1] 82 rigid atoms, others: [12, 13, 14, 15, 16, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 214 number of broken/clashed sets: 81 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220961 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C(=O)[O-])=C(Cl)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 54, 54, 54, 74, 74, 54, 54, 54, 1, 2, 2, 2, 3, 3, 1, 12, 12, 54] 82 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 182 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220961 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220961 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220961/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220961 Building REAL300000220962 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220962' /scratch/stefan/7769890/working/building/REAL300000220962 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220962 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220962/0 /scratch/stefan/7769890/working/building/REAL300000220962 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/977 `/scratch/stefan/7769890/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C#N)=CC(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220962 none CC1=CC(C#N)=CC(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 8, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 3, 3, 2, 2, 2, 1] 15 rigid atoms, others: [39, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220962 none CC1=CC(C#N)=CC(C)=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', '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, 8, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 15, 15, 15, 10, 10, 10, 2, 2, 2, 1, 1, 2, 2, 2, 4, 4, 15, 15, 10, 10, 10, 9] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220962 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220962 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220962/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220962 Building REAL300000220963 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220963' /scratch/stefan/7769890/working/building/REAL300000220963 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220963 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220963/0 /scratch/stefan/7769890/working/building/REAL300000220963 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/978 `/scratch/stefan/7769890/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=CS1) `REAL300000220963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220963 none COC(=O)C1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 73, 169, 73, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 73, 73, 73, 169, 169, 169, 11, 11, 2, 2, 2, 3, 3, 1, 73, 73] 201 rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 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: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220963 none COC(=O)C1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 9, 9, 73, 73, 73, 73, 73, 124, 144, 144, 73, 73, 73, 1, 1, 1, 13, 13, 13, 9, 9, 73, 73, 73, 124, 124, 73, 1, 1] 201 rigid atoms, others: [2, 35, 4, 5, 6, 34, 20, 21, 22] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 507 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220963 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220963 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220963/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220963 Building REAL300000220964 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220964' /scratch/stefan/7769890/working/building/REAL300000220964 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220964 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220964/0 /scratch/stefan/7769890/working/building/REAL300000220964 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/979 `/scratch/stefan/7769890/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CCF)N=C2)N1) `REAL300000220964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220964 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CCF)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 15, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 91, 135, 135, 56, 57, 56, 7, 7, 1, 1, 1, 1, 1, 7, 17, 1, 1, 57, 57, 57, 57, 91, 91, 7, 7, 1, 7, 7, 17, 17, 1, 57] 201 rigid atoms, others: [34, 12, 13, 14, 15, 16, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 35]) total number of confs: 511 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220964 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN(CCF)N=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 15, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 57, 57, 57, 135, 172, 57, 57, 1, 2, 2, 2, 3, 3, 12, 12, 57, 135, 135, 172, 172, 57, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 21] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 673 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220964 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220964 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220964/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220964 Building REAL300000220965 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220965' /scratch/stefan/7769890/working/building/REAL300000220965 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220965 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220965/0 /scratch/stefan/7769890/working/building/REAL300000220965 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/980 `/scratch/stefan/7769890/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Cl) `REAL300000220965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220965 none CC1=NN(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [41, 41, 41, 41, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 11, 11, 2, 2, 2, 3, 3, 1] 46 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 86 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220965 none CC1=NN(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 1, 1, 1, 9, 9, 41, 41, 41, 41, 41, 46, 46, 46, 41, 41, 41, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 41, 41, 41, 46, 46, 41] 46 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220965 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220965 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220965/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220965 Building REAL300000220966 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220966' /scratch/stefan/7769890/working/building/REAL300000220966 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220966 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220966/0 /scratch/stefan/7769890/working/building/REAL300000220966 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/981 `/scratch/stefan/7769890/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2C2CCCC2)=N1) `REAL300000220966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220966 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2C2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 130, 161, 161, 74, 74, 74, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 74, 74, 74, 74, 130, 130, 74, 9, 9, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 573 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220966 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2C2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 74, 74, 74, 74, 74, 74, 135, 135, 135, 135, 1, 2, 2, 2, 3, 3, 1, 12, 12, 74, 74, 74, 74, 135, 135, 135, 135, 135, 135, 135, 135, 135] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 30] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 343 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220966 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C)N=C2C2CCCC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 135, 201, 201, 201, 135, 135, 135, 37, 37, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 201, 201, 135, 37, 37, 7, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 607 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220966 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220966 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220966/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220966 Building REAL300000220967 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220967' /scratch/stefan/7769890/working/building/REAL300000220967 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220967 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220967/0 /scratch/stefan/7769890/working/building/REAL300000220967 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/982 `/scratch/stefan/7769890/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Br) `REAL300000220967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220967 none CC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [29, 29, 19, 29, 29, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 29, 29, 29, 29, 29, 27, 29, 29, 11, 11, 2, 2, 2, 3, 3, 1] 37 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 110 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: REAL300000220967 none CC1=CC=CC(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 37, 37, 37, 29, 29, 29, 1, 1, 2, 2, 2, 1, 1, 1, 7, 7, 29, 29, 29, 37, 37, 29] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220967 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220967 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220967/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220967 Building REAL300000220968 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220968' /scratch/stefan/7769890/working/building/REAL300000220968 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220968 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220968/0 /scratch/stefan/7769890/working/building/REAL300000220968 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/983 `/scratch/stefan/7769890/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)=N1) `REAL300000220968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220968 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 52, 54, 54, 33, 33, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 1, 33, 33, 33, 33, 52, 52, 33, 5, 5, 1, 1, 1, 10, 10, 10, 10, 1] 201 rigid atoms, others: [36, 37, 38, 43, 12, 13, 14, 15, 16, 17, 18, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220968 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 33, 33, 33, 33, 33, 116, 127, 127, 127, 127, 127, 127, 33, 1, 2, 2, 2, 3, 3, 1, 10, 10, 33, 33, 33, 127, 127, 127, 127, 33] 201 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 207 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220968 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 201, 201, 201, 127, 127, 127, 34, 34, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 127, 127, 127, 127, 201, 201, 127, 34, 34, 10, 10, 10, 1, 1, 1, 1, 10] 201 rigid atoms, others: [39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43]) total number of confs: 642 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220968 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220968 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220968/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220968 Building REAL300000220969 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220969' /scratch/stefan/7769890/working/building/REAL300000220969 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220969 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220969/0 /scratch/stefan/7769890/working/building/REAL300000220969 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/984 `/scratch/stefan/7769890/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCCCC3=C2)N1) `REAL300000220969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220969 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 29, 29, 29, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 29, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16] 29 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 40, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 106 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220969 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OCCCC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 3, 3, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 40, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 56 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220969 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220969 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220969/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220969 Building REAL300000220970 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220970' /scratch/stefan/7769890/working/building/REAL300000220970 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220970 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220970/0 /scratch/stefan/7769890/working/building/REAL300000220970 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/985 `/scratch/stefan/7769890/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C(=O)N(C)C)=C2)N1) `REAL300000220970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220970 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C(=O)N(C)C)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 73, 88, 88, 41, 41, 41, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 1, 41, 41, 41, 41, 73, 73, 6, 6, 1, 1, 1, 15, 15, 15, 15, 15, 15, 1, 41] 145 rigid atoms, others: [32, 33, 34, 41, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 343 number of broken/clashed sets: 145 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220970 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC(C(=O)N(C)C)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 12, 12, 41, 41, 41, 41, 41, 98, 98, 108, 108, 41, 1, 2, 2, 2, 3, 3, 12, 12, 41, 41, 41, 108, 108, 108, 108, 108, 108, 41, 1] 145 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 24, 42] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 307 number of broken/clashed sets: 145 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220970 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220970 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220970/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220970 Building REAL300000220971 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220971' /scratch/stefan/7769890/working/building/REAL300000220971 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220971 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220971/0 /scratch/stefan/7769890/working/building/REAL300000220971 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/986 `/scratch/stefan/7769890/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(C)=NO1) `REAL300000220971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220971 none CCC1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 8, 12, 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, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [95, 57, 57, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 57, 57, 57, 57, 95, 95, 95, 95, 95, 12, 12, 2, 2, 2, 3, 3, 1, 57, 57, 57] 139 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 322 number of broken/clashed sets: 138 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220971 none CCC1=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)C(C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 5, 8, 12, 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, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 13, 13, 57, 57, 57, 57, 57, 93, 103, 103, 57, 57, 57, 1, 1, 1, 1, 8, 8, 8, 7, 7, 13, 13, 57, 57, 57, 93, 93, 57, 2, 2, 2] 139 rigid atoms, others: [1, 2, 3, 4, 18, 19, 20, 21] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 372 number of broken/clashed sets: 138 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220971 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220971 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220971/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220971 Building REAL300000220972 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220972' /scratch/stefan/7769890/working/building/REAL300000220972 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220972 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220972/0 /scratch/stefan/7769890/working/building/REAL300000220972 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/987 `/scratch/stefan/7769890/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)N=C2N(C)C)=N1) `REAL300000220972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220972 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)N=C2N(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 8, 5, 5, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 65, 65, 65, 45, 45, 45, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 45, 45, 45, 45, 65, 65, 45, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5] 65 rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 203 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220972 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)(F)F)N=C2N(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 8, 5, 5, 8, 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, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 52, 52, 1, 2, 2, 2, 3, 3, 1, 11, 11, 45, 45, 52, 52, 52, 52, 52, 52] 65 rigid atoms, others: [0, 1, 2, 3, 32, 7, 8, 9, 10, 11, 26] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 119 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220972 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220972 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220972/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220972 Building REAL300000220973 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220973' /scratch/stefan/7769890/working/building/REAL300000220973 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220973 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220973/0 /scratch/stefan/7769890/working/building/REAL300000220973 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/988 `/scratch/stefan/7769890/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC(C3=CC=CC=N3)=N2)N1) `REAL300000220973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220973 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC(C3=CC=CC=N3)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 98, 135, 135, 54, 54, 54, 11, 11, 1, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 1, 54, 55, 55, 55, 98, 98, 11, 11, 1, 1, 13, 13, 12, 13, 54] 201 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 503 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220973 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC(C3=CC=CC=N3)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 54, 54, 54, 54, 54, 146, 146, 145, 146, 146, 54, 1, 2, 2, 2, 3, 3, 11, 11, 54, 54, 146, 146, 145, 146, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 25, 39] set([4, 5, 6, 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: 238 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220973 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NC(C3=CC=CC=N3)=N2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 201, 201, 201, 146, 146, 146, 65, 65, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 146, 146, 146, 146, 201, 201, 65, 65, 12, 13, 1, 1, 1, 1, 146] 201 rigid atoms, others: [35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 595 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220973 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220973 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220973/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220973 Building REAL300000220974 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220974' /scratch/stefan/7769890/working/building/REAL300000220974 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220974 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220974/0 /scratch/stefan/7769890/working/building/REAL300000220974 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/989 `/scratch/stefan/7769890/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N=C1) `REAL300000220974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220974 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [88, 88, 52, 88, 52, 52, 52, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 52, 52, 88, 88, 88, 52, 52, 11, 11, 2, 2, 2, 3, 3, 1, 52] 115 rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 222 number of broken/clashed sets: 114 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220974 none COC(=O)C1=CC=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 52, 52, 52, 52, 52, 75, 77, 77, 52, 52, 52, 1, 1, 12, 12, 12, 1, 1, 11, 11, 52, 52, 52, 75, 75, 52, 1] 115 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 27, 28, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 243 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220974 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220974 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220974/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220974 Building REAL300000220975 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220975' /scratch/stefan/7769890/working/building/REAL300000220975 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220975 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220975/0 /scratch/stefan/7769890/working/building/REAL300000220975 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/990 `/scratch/stefan/7769890/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C(F)(F)F)=N2)=N1) `REAL300000220975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220975 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C(F)(F)F)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 5, 15, 15, 15, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 41, 41, 41, 35, 35, 35, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 35, 35, 35, 35, 41, 41, 33, 10, 10, 1] 41 rigid atoms, others: [12, 13, 14, 15, 16, 17, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 98 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220975 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CSC(C(F)(F)F)=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 5, 15, 15, 15, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 1, 12, 12, 35] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 83 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220975 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220975 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220975/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220975 Building REAL300000220976 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220976' /scratch/stefan/7769890/working/building/REAL300000220976 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220976 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220976/0 /scratch/stefan/7769890/working/building/REAL300000220976 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/991 `/scratch/stefan/7769890/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1) `REAL300000220976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220976 none CC1=C(C(=O)[O-])C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 55, 55, 38, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 38, 38, 38, 38, 38, 11, 11, 2, 2, 2, 3, 3, 1] 78 rigid atoms, others: [34, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 152 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: REAL300000220976 none CC1=C(C(=O)[O-])C=C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 3, 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, 3, 3, 1, 1, 1, 10, 10, 38, 38, 38, 38, 38, 52, 78, 78, 38, 38, 38, 1, 2, 2, 2, 1, 10, 10, 38, 38, 38, 52, 52, 38] 78 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 22, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 259 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220976 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220976 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220976/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220976 Building REAL300000220977 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220977' /scratch/stefan/7769890/working/building/REAL300000220977 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220977 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220977/0 /scratch/stefan/7769890/working/building/REAL300000220977 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/992 `/scratch/stefan/7769890/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)=N1) `REAL300000220977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220977 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [56, 56, 56, 56, 83, 92, 92, 56, 56, 56, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 2, 2, 7, 7, 7, 7, 1, 56, 56, 56, 56, 83, 83, 56, 12, 12, 1, 1, 7, 7, 7, 7] 104 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 303 number of broken/clashed sets: 103 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220977 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 56, 56, 56, 56, 90, 90, 76, 78, 90, 90, 90, 90, 56, 1, 2, 2, 2, 3, 3, 1, 12, 12, 56, 56, 90, 90, 90, 90] 104 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 27] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 253 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220977 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [90, 90, 90, 90, 104, 104, 104, 90, 90, 90, 42, 42, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 90, 90, 90, 90, 104, 104, 90, 42, 42, 7, 7, 1, 1, 1, 1] 104 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 249 number of broken/clashed sets: 103 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220977 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220977 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220977/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220977 Building REAL300000220978 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220978' /scratch/stefan/7769890/working/building/REAL300000220978 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220978 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220978/0 /scratch/stefan/7769890/working/building/REAL300000220978 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/993 `/scratch/stefan/7769890/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CN=C1F) `REAL300000220978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220978 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CN=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 6, 5, 3, 3, 2, 2, 2, 1, 16] 29 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34]) total number of confs: 52 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: REAL300000220978 none CC1=CC(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=CN=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 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, 5, 5, 16, 16, 16, 16, 16, 29, 29, 29, 16, 16, 16, 1, 1, 1, 1, 2, 2, 2, 1, 5, 5, 29, 29, 16, 16, 16, 16, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 34, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220978 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220978 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220978/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220978 Building REAL300000220979 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220979' /scratch/stefan/7769890/working/building/REAL300000220979 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220979 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220979/0 /scratch/stefan/7769890/working/building/REAL300000220979 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/994 `/scratch/stefan/7769890/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=NC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1) `REAL300000220979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220979 none CC1=CC(F)=NC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 23, 23, 23, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 23, 23, 23, 23, 23, 11, 11, 3, 3, 2, 2, 2, 1] 31 rigid atoms, others: [34, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 67 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: REAL300000220979 none CC1=CC(F)=NC=C1C=CC1=NC(=O)C(CC(=O)[O-])=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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, 1, 1, 7, 7, 23, 23, 23, 23, 23, 31, 31, 31, 23, 23, 23, 2, 2, 2, 1, 1, 7, 7, 31, 31, 23, 23, 23, 21] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220979 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220979 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220979/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220979 Building REAL300000220980 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220980' /scratch/stefan/7769890/working/building/REAL300000220980 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220980 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220980/0 /scratch/stefan/7769890/working/building/REAL300000220980 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/995 `/scratch/stefan/7769890/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)F)C(F)=C2)=N1) `REAL300000220980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220980 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)F)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 33, 33, 33, 57, 71, 71, 33, 33, 33, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 33, 33, 33, 33, 57, 57, 33, 5, 5, 1, 1, 11, 1] 89 rigid atoms, others: [32, 33, 35, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 276 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220980 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C(F)F)C(F)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 15, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 33, 33, 33, 33, 73, 73, 33, 33, 33, 1, 2, 2, 2, 3, 3, 1, 10, 10, 33, 33, 73, 33] 89 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 272 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220980 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220980 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220980/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220980 Building REAL300000220981 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220981' /scratch/stefan/7769890/working/building/REAL300000220981 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220981 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220981/0 /scratch/stefan/7769890/working/building/REAL300000220981 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/996 `/scratch/stefan/7769890/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C(=O)[O-])=NN2C)N1) `REAL300000220981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220981 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C(=O)[O-])=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 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, 24, 24, 24, 43, 43, 43, 24, 24, 24, 9, 9, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 24, 24, 24, 24, 43, 43, 9, 9, 1, 2, 2, 2, 24] 43 rigid atoms, others: [12, 13, 14, 15, 16, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 165 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: REAL300000220981 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC(C(=O)[O-])=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 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: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 3, 10, 10, 24, 24, 24, 24, 1] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220981 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220981 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220981/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220981 Building REAL300000220982 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220982' /scratch/stefan/7769890/working/building/REAL300000220982 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220982 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220982/0 /scratch/stefan/7769890/working/building/REAL300000220982 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/997 `/scratch/stefan/7769890/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=N1) `REAL300000220982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220982 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 87, 128, 128, 63, 63, 63, 13, 13, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 63, 63, 63, 63, 87, 87, 63, 13, 13, 1, 1, 12, 12, 24, 12] 402 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 432 number of broken/clashed sets: 400 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220982 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 63, 63, 63, 63, 174, 174, 174, 174, 174, 174, 174, 174, 174, 63, 1, 2, 2, 2, 3, 3, 1, 12, 12, 63, 63, 174, 174, 348, 174] 402 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 34, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 606 number of broken/clashed sets: 400 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220982 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 174, 201, 201, 201, 174, 174, 174, 56, 56, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 174, 174, 174, 174, 201, 201, 174, 56, 56, 12, 12, 1, 1, 2, 1] 402 rigid atoms, others: [39, 40, 42, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 440 number of broken/clashed sets: 400 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220982 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220982 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220982/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220982 Building REAL300000220983 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220983' /scratch/stefan/7769890/working/building/REAL300000220983 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220983 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220983/0 /scratch/stefan/7769890/working/building/REAL300000220983 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/998 `/scratch/stefan/7769890/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C)=C1) `REAL300000220983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220983 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [40, 22, 22, 28, 28, 11, 11, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 28, 28, 28, 40, 40, 40, 28, 28, 11, 11, 3, 3, 2, 2, 2, 1, 28, 28, 28, 28] 56 rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 118 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: REAL300000220983 none COC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 41, 56, 56, 28, 28, 28, 1, 1, 1, 2, 2, 2, 1, 1, 7, 7, 41, 41, 28, 28, 28, 28, 2, 2, 2, 1] 56 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220983 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220983 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220983/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220983 Building REAL300000220984 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220984' /scratch/stefan/7769890/working/building/REAL300000220984 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220984 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220984/0 /scratch/stefan/7769890/working/building/REAL300000220984 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/999 `/scratch/stefan/7769890/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(C)=C2Cl)=N1) `REAL300000220984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220984 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(C)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 5, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 31, 31, 31, 17, 17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 31, 31, 17, 7, 7, 1, 1, 2, 2, 2] 31 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 121 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: REAL300000220984 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC=C(Cl)C(C)=C2Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 5, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 3, 3, 1, 9, 9, 17, 17, 17, 17, 17] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 58 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220984 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220984 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220984/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220984 Building REAL300000220985 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220985' /scratch/stefan/7769890/working/building/REAL300000220985 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220985 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220985/0 /scratch/stefan/7769890/working/building/REAL300000220985 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1000 `/scratch/stefan/7769890/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C#N)=CC=C2Br)=N1) `REAL300000220985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220985 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C#N)=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 39, 39, 39, 49, 49, 49, 39, 39, 39, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 49, 49, 39, 9, 9, 1, 1, 1] 49 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 115 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: REAL300000220985 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CC(C#N)=CC=C2Br)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 3, 7, 7, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 3, 3, 1, 11, 11, 39, 39, 39] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220985 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220985 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220985/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220985 Building REAL300000220986 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220986' /scratch/stefan/7769890/working/building/REAL300000220986 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220986 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220986/0 /scratch/stefan/7769890/working/building/REAL300000220986 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1001 `/scratch/stefan/7769890/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OC(C)CC3=C2)N1) `REAL300000220986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220986 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OC(C)CC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 26, 26, 26, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 26, 26, 6, 6, 1, 1, 1, 2, 2, 2, 1, 1, 1, 19] 26 rigid atoms, others: [32, 33, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 40]) total number of confs: 79 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: REAL300000220986 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=C3OC(C)CC3=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 6, 6, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 40, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 59 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220986 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220986 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220986/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220986 Building REAL300000220987 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220987' /scratch/stefan/7769890/working/building/REAL300000220987 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220987 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220987/0 /scratch/stefan/7769890/working/building/REAL300000220987 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1002 `/scratch/stefan/7769890/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OC(=O)N3)N1) `REAL300000220987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220987 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OC(=O)N3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 4, 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: [39, 39, 39, 39, 55, 55, 55, 39, 39, 39, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 55, 55, 11, 11, 1, 1, 1, 1, 39] 55 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 157 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220987 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OC(=O)N3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 3, 3, 11, 11, 39, 39, 39, 39, 1] 55 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 35, 23] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 81 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220987 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220987 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220987/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220987 Building REAL300000220988 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220988' /scratch/stefan/7769890/working/building/REAL300000220988 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220988 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220988/0 /scratch/stefan/7769890/working/building/REAL300000220988 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1003 `/scratch/stefan/7769890/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCC3)N1) `REAL300000220988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220988 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCC3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 48, 48, 48, 38, 38, 38, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 48, 48, 11, 11, 1, 1, 1, 1, 1, 1, 1, 38] 48 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 37]) total number of confs: 118 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: REAL300000220988 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC3=C2OCC3)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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, 3, 5, 5, 1, 1, 1, 1, 1, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38, 1, 2, 2, 2, 3, 3, 9, 9, 38, 38, 38, 38, 38, 38, 38, 1] 48 rigid atoms, others: [0, 1, 2, 3, 37, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220988 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220988 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220988/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220988 Building REAL300000220989 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220989' /scratch/stefan/7769890/working/building/REAL300000220989 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220989 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220989/0 /scratch/stefan/7769890/working/building/REAL300000220989 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1004 `/scratch/stefan/7769890/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1) `REAL300000220989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220989 none CSCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [107, 64, 24, 24, 44, 44, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 44, 44, 107, 107, 107, 64, 64, 44, 44, 12, 12, 3, 3, 2, 2, 2, 1, 44, 44] 145 rigid atoms, others: [37, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 399 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: REAL300000220989 none CSCC1=CC=C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [18, 4, 1, 1, 1, 1, 1, 1, 6, 6, 44, 44, 44, 44, 44, 72, 101, 101, 44, 44, 44, 1, 1, 18, 18, 18, 4, 4, 1, 1, 6, 6, 72, 72, 44, 44, 44, 44, 1, 1] 145 rigid atoms, others: [2, 3, 4, 5, 6, 7, 39, 21, 22, 38, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 370 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220989 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220989 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220989/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220989 Building REAL300000220990 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220990' /scratch/stefan/7769890/working/building/REAL300000220990 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220990 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220990/0 /scratch/stefan/7769890/working/building/REAL300000220990 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1005 `/scratch/stefan/7769890/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3CCC3)N=C2)=N1) `REAL300000220990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220990 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3CCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 66, 89, 89, 42, 42, 42, 7, 7, 1, 1, 1, 1, 1, 8, 18, 18, 18, 1, 1, 42, 42, 42, 42, 66, 66, 42, 7, 7, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 1] 201 rigid atoms, others: [32, 42, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 346 number of broken/clashed sets: 200 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220990 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3CCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 42, 42, 42, 107, 155, 155, 155, 42, 42, 1, 2, 2, 2, 3, 3, 1, 11, 11, 42, 107, 107, 155, 155, 155, 155, 155, 155, 155, 42] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 551 number of broken/clashed sets: 200 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220990 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(CC3CCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 155, 155, 155, 201, 201, 201, 155, 155, 155, 56, 56, 18, 18, 18, 5, 1, 1, 1, 1, 1, 18, 18, 155, 155, 155, 155, 201, 201, 155, 56, 56, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 18] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42]) total number of confs: 550 number of broken/clashed sets: 200 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220990 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220990 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220990/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220990 Building REAL300000220991 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220991' /scratch/stefan/7769890/working/building/REAL300000220991 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220991 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220991/0 /scratch/stefan/7769890/working/building/REAL300000220991 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1006 `/scratch/stefan/7769890/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C3COCCC3=NN2C)=N1) `REAL300000220991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220991 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C3COCCC3=NN2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 50, 50, 37, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40]) total number of confs: 128 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: REAL300000220991 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=C3COCCC3=NN2C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 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 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, 3, 5, 5, 1, 1, 1, 1, 1, 12, 12, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 3, 3, 1, 12, 12, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 23, 29] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 85 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220991 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220991 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220991/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220991 Building REAL300000220992 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220992' /scratch/stefan/7769890/working/building/REAL300000220992 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220992 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220992/0 /scratch/stefan/7769890/working/building/REAL300000220992 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1007 `/scratch/stefan/7769890/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3CCCC3=NN2C)N1) `REAL300000220992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220992 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3CCCC3=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 50, 50, 50, 36, 36, 36, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 36] 50 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39]) total number of confs: 145 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: REAL300000220992 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=C3CCCC3=NN2C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 36, 36, 36, 36, 36, 36, 36, 36, 1, 2, 2, 2, 3, 3, 11, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1] 50 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220992 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220992 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220992/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220992 Building REAL300000220993 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220993' /scratch/stefan/7769890/working/building/REAL300000220993 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220993 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220993/0 /scratch/stefan/7769890/working/building/REAL300000220993 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1008 `/scratch/stefan/7769890/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2CCC2)N1) `REAL300000220993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220993 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2CCC2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 111, 122, 122, 71, 71, 71, 10, 10, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 71, 71, 71, 71, 111, 111, 10, 10, 1, 1, 9, 9, 9, 9, 9, 9, 9, 71] 161 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 393 number of broken/clashed sets: 160 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220993 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2CCC2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 1, 12, 12, 71, 71, 71, 71, 71, 122, 122, 122, 1, 2, 2, 2, 3, 3, 12, 12, 71, 71, 122, 122, 122, 122, 122, 122, 122, 1] 161 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 39] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 298 number of broken/clashed sets: 160 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220993 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=NN2C2CCC2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 122, 161, 161, 161, 122, 122, 122, 42, 42, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 122, 122, 122, 122, 161, 161, 42, 42, 9, 9, 1, 1, 1, 1, 1, 1, 1, 122] 161 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39]) total number of confs: 430 number of broken/clashed sets: 160 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220993 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220993 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220993/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220993 Building REAL300000220994 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220994' /scratch/stefan/7769890/working/building/REAL300000220994 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220994 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220994/0 /scratch/stefan/7769890/working/building/REAL300000220994 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1009 `/scratch/stefan/7769890/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3CCC3)N=C2)=N1) `REAL300000220994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220994 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3CCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 61, 89, 89, 39, 39, 39, 6, 6, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 39, 39, 39, 39, 61, 61, 39, 6, 6, 1, 12, 12, 12, 12, 12, 12, 12, 1] 141 rigid atoms, others: [39, 12, 13, 14, 15, 16, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 320 number of broken/clashed sets: 140 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220994 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3CCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 108, 108, 108, 39, 39, 1, 2, 2, 2, 3, 3, 1, 11, 11, 39, 108, 108, 108, 108, 108, 108, 108, 39] 141 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 22, 28] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 272 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220994 none CC1=C(CC(=O)[O-])C(=O)NC(C=CC2=CN(C3CCC3)N=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 141, 141, 141, 108, 108, 108, 43, 43, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 108, 108, 108, 108, 141, 141, 108, 43, 43, 12, 1, 1, 1, 1, 1, 1, 1, 12] 141 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39]) total number of confs: 388 number of broken/clashed sets: 140 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220994 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220994 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220994/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220994 Building REAL300000220995 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220995' /scratch/stefan/7769890/working/building/REAL300000220995 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220995 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220995/0 /scratch/stefan/7769890/working/building/REAL300000220995 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1010 `/scratch/stefan/7769890/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)OC1=CC=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220995 none COC(=O)C(C)OC1=CC=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 103, 140, 66, 103, 30, 30, 30, 19, 30, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 140, 140, 140, 103, 103, 103, 103, 30, 30, 30, 30, 9, 9, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [45, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 506 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220995 none COC(=O)C(C)OC1=CC=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 14, 21, 6, 14, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 30, 30, 30, 30, 30, 51, 79, 79, 30, 30, 30, 21, 21, 21, 14, 14, 14, 14, 1, 1, 1, 1, 8, 8, 30, 30, 30, 51, 51, 30] 201 rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 355 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220995 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220995 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220995/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220995 Building REAL300000220996 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220996' /scratch/stefan/7769890/working/building/REAL300000220996 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220996 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220996/0 /scratch/stefan/7769890/working/building/REAL300000220996 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1011 `/scratch/stefan/7769890/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)COC1=CC=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1) `REAL300000220996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220996 none COC(=O)COC1=CC=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 118, 169, 63, 32, 32, 32, 19, 32, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 169, 169, 169, 118, 118, 32, 32, 32, 32, 9, 9, 2, 2, 2, 3, 3, 1] 201 rigid atoms, others: [42, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 576 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220996 none COC(=O)COC1=CC=CC=C1C=CC1=NC(C)=C(CC(=O)[O-])C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 36, 89, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 32, 57, 74, 74, 32, 32, 32, 89, 89, 89, 36, 36, 1, 1, 1, 1, 7, 7, 32, 32, 32, 57, 57, 32] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 530 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220996 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220996 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220996/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220996 Building REAL300000220997 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220997' /scratch/stefan/7769890/working/building/REAL300000220997 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220997 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220997/0 /scratch/stefan/7769890/working/building/REAL300000220997 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1012 `/scratch/stefan/7769890/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=CC(C(=O)[O-])=C2)N1) `REAL300000220997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220997 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=CC(C(=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 4, 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: [21, 21, 21, 21, 31, 31, 31, 21, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 21, 21, 31, 31, 6, 6, 1, 1, 1, 21] 31 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 97 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: REAL300000220997 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CN=CC(C(=O)[O-])=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 4, 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, 3, 7, 7, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 9, 9, 21, 21, 21, 1] 31 rigid atoms, others: [0, 1, 2, 3, 33, 7, 8, 9, 10, 11, 22] set([4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 65 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220997 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220997 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220997/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220997 Building REAL300000220998 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220998' /scratch/stefan/7769890/working/building/REAL300000220998 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220998 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220998/0 /scratch/stefan/7769890/working/building/REAL300000220998 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1013 `/scratch/stefan/7769890/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC2=CC=CC(F)=C2)N1) `REAL300000220998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220998 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC2=CC=CC(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 68, 91, 91, 40, 40, 40, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 40, 40, 40, 40, 68, 68, 9, 9, 1, 1, 1, 1, 15, 15, 15, 15, 40] 201 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 339 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220998 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC2=CC=CC(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 7, 7, 40, 40, 14, 40, 40, 40, 92, 141, 141, 141, 141, 141, 141, 1, 2, 2, 2, 3, 3, 7, 7, 40, 40, 40, 40, 141, 141, 141, 141, 1] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 11, 43, 27] set([4, 5, 6, 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, 41, 42]) total number of confs: 330 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220998 none CC1=C(CC(=O)[O-])C(=O)N=C(C=CC2=CC=CC=C2OC2=CC=CC(F)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', '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, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 141, 201, 201, 201, 141, 141, 141, 52, 52, 15, 15, 15, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 201, 201, 52, 52, 15, 15, 15, 15, 1, 1, 1, 1, 141] 201 rigid atoms, others: [39, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43]) total number of confs: 604 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220998 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220998 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220998/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220998 Building REAL300000220999 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000220999' /scratch/stefan/7769890/working/building/REAL300000220999 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000220999 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000220999/0 /scratch/stefan/7769890/working/building/REAL300000220999 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1014 `/scratch/stefan/7769890/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Br) `REAL300000220999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000220999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000220999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220999 none COC1=CC=C(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [63, 41, 41, 41, 41, 41, 41, 13, 13, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 41, 41, 63, 63, 63, 41, 41, 41, 41, 41, 13, 13, 2, 2, 2, 3, 3, 1] 77 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 138 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000220999 none COC1=CC=C(C)C(C=CC2=NC(C)=C(CC(=O)[O-])C(=O)N2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 1, 11, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 41, 41, 63, 77, 77, 41, 41, 41, 1, 1, 4, 4, 4, 1, 1, 2, 2, 2, 7, 7, 41, 41, 41, 63, 63, 41] 77 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 253 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000220999 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000220999 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000220999/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000220999 Building REAL300000221000 mkdir: created directory `/scratch/stefan/7769890/working/building/REAL300000221000' /scratch/stefan/7769890/working/building/REAL300000221000 /scratch/stefan/7769890/working /scratch/stefan/7769890 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000221000 mkdir: created directory `0' /scratch/stefan/7769890/working/building/REAL300000221000/0 /scratch/stefan/7769890/working/building/REAL300000221000 /scratch/stefan/7769890/working /scratch/stefan/7769890 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7769890/working/3D/1015 `/scratch/stefan/7769890/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1) `REAL300000221000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000221000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769890/working/building/REAL300000221000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000221000 none COC1=CC=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [69, 41, 41, 41, 41, 41, 41, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 41, 69, 69, 69, 41, 41, 41, 41, 41, 10, 10, 3, 3, 2, 2, 2, 1, 41] 79 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 141 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: REAL300000221000 none COC1=CC=C(C)C(C=CC2=NC(=O)C(CC(=O)[O-])=C(C)N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 1, 5, 1, 11, 11, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 41, 41, 63, 73, 73, 41, 41, 41, 1, 3, 3, 3, 1, 1, 2, 2, 2, 7, 7, 63, 63, 41, 41, 41, 39, 1] 79 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 39, 22, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 238 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769890/working/building/REAL300000221000 /scratch/stefan/7769890/working /scratch/stefan/7769890 Finished preparing REAL300000221000 Recording results /scratch/stefan/7769890/working /scratch/stefan/7769890 Appending to /scratch/stefan/7769890/finished/xaaaaim.* 0: /scratch/stefan/7769890/working/building/REAL300000221000/0.* Removing working files in /scratch/stefan/7769890/working/building/REAL300000221000 /scratch/stefan/7769890 Compressing combined databse files /scratch/stefan/7769890/finished/xaaaaim.db2.gz /scratch/stefan/7769890/finished/xaaaaim.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7769890/finished) ======================================================= Finalizing... removed `/scratch/stefan/7769890/working/3D/1016' removed directory: `/scratch/stefan/7769890/working/3D' `/scratch/stefan/7769890/working/protonate' -> `/scratch/stefan/7769890/archive' `/scratch/stefan/7769890/working/input-smiles.ism' -> `/scratch/stefan/7769890/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7769890/working/building' rmdir: removing directory, `/scratch/stefan/7769890/working' ls: No match. ls: No match.